-
1
-
-
84872007514
-
Architecture of the major component of the type III secretion system export apparatus
-
doi: 10.1038/nsmb.2452
-
Abrusci P, Vergara-Irigaray M, Johnson S, Beeby MD, Hendrixson DR, Roversi P, et al. 2013. Architecture of the major component of the type III secretion system export apparatus. Nat Struct Mol Biol 20:99-104. doi: 10.1038/nsmb.2452.
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 99-104
-
-
Abrusci, P.1
Vergara-Irigaray, M.2
Johnson, S.3
Beeby, M.D.4
Hendrixson, D.R.5
Roversi, P.6
-
2
-
-
0029021928
-
Structural plasticity of the nuclear pore complex
-
doi: 10.1016/S0022-2836(95)80050-6
-
Akey CW. 1995. Structural plasticity of the nuclear pore complex. J Mol Biol 248:273-93. doi: 10.1016/S0022-2836(95)80050-6.
-
(1995)
J Mol Biol
, vol.248
, pp. 273-293
-
-
Akey, C.W.1
-
3
-
-
36749045172
-
The molecular architecture of the nuclear pore complex
-
doi: 10.1038/nature06405
-
Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, et al. 2007. The molecular architecture of the nuclear pore complex. Nature 450:695-701. doi: 10.1038/nature06405.
-
(2007)
Nature
, vol.450
, pp. 695-701
-
-
Alber, F.1
Dokudovskaya, S.2
Veenhoff, L.M.3
Zhang, W.4
Kipper, J.5
Devos, D.6
-
4
-
-
0029116599
-
VirG, a Yersinia enterocolitica lipoprotein involved in Ca2+ dependency, is related to exsB of Pseudomonas aeruginosa
-
Allaoui A, Scheen R, Lambert de Rouvroit C, Cornelis GR. 1995. VirG, a Yersinia enterocolitica lipoprotein involved in Ca2+ dependency, is related to exsB of Pseudomonas aeruginosa. J Bacteriol 177:4230-7.
-
(1995)
J Bacteriol
, vol.177
, pp. 4230-4237
-
-
Allaoui, A.1
Scheen, R.2
de Rouvroit, L.C.3
Cornelis, G.R.4
-
5
-
-
0027441950
-
Essential dynamics of proteins
-
doi: 10.1002/prot.340170408
-
Amadei A, Linssen ABM, Berendsen HJC. 1993. Essential dynamics of proteins. Proteins 17:412-25. doi: 10.1002/prot.340170408.
-
(1993)
Proteins
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.M.2
Berendsen, H.J.C.3
-
6
-
-
79955796983
-
Stochastic conformational pumping: A mechanism for free-energy transduction by molecules
-
doi: 10.1146/annurev-biophys-042910-155355
-
Astumian RD. 2011. Stochastic conformational pumping: a mechanism for free-energy transduction by molecules. Ann Rev Biophys 40:289-313. doi: 10.1146/annurev-biophys-042910-155355.
-
(2011)
Ann Rev Biophys
, vol.40
, pp. 289-313
-
-
Astumian, R.D.1
-
7
-
-
77949634796
-
Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins
-
doi: 10.1021/cr900095e
-
Bahar I, Lezon TR, Bakan A, Shrivastava IH. 2009. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 110:1463-97. doi: 10.1021/cr900095e.
-
(2009)
Chem Rev
, vol.110
, pp. 1463-1497
-
-
Bahar, I.1
Lezon, T.R.2
Bakan, A.3
Shrivastava, I.H.4
-
8
-
-
77952938726
-
Global dynamics of proteins: Bridging between structure and function
-
doi: 10.1146/annurev.biophys.093008.131258
-
Bahar I, Lezon TR, Yang L-W, Eyal E. 2010. Global dynamics of proteins: bridging between structure and function. Ann Rev Biophys 39:23-42. doi: 10.1146/annurev.biophys.093008.131258.
-
(2010)
Ann Rev Biophys
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Yang, L.-W.3
Eyal, E.4
-
9
-
-
79957788878
-
ProDy: Protein dynamics inferred from theory and experiments
-
doi: 10.1093/bioinformatics/btr168
-
Bakan A, Meireles LM, Bahar I. 2011. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 27:1575-7. doi: 10.1093/bioinformatics/btr168.
-
(2011)
Bioinformatics
, vol.27
, pp. 1575-1577
-
-
Bakan, A.1
Meireles, L.M.2
Bahar, I.3
-
10
-
-
84858002430
-
Type VI secretion requires a dynamic contractile phage tail-like structure
-
doi: 10.1038/nature10846
-
Basler M, Pilhofer M, Henderson GP, Jensen GJ, Mekalanos JJ. 2012. Type VI secretion requires a dynamic contractile phage tail-like structure. Nature 483:182-6. doi: 10.1038/nature10846.
-
(2012)
Nature
, vol.483
, pp. 182-186
-
-
Basler, M.1
Pilhofer, M.2
Henderson, G.P.3
Jensen, G.J.4
Mekalanos, J.J.5
-
11
-
-
34948891095
-
Snapshots of nuclear pore complexes in action captured by cryo-electron tomography
-
doi: 10.1038/nature06170
-
Beck M, Lucic V, Forster F, Baumeister W, Medalia O. 2007. Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449:611-5. doi: 10.1038/nature06170.
-
(2007)
Nature
, vol.449
, pp. 611-615
-
-
Beck, M.1
Lucic, V.2
Forster, F.3
Baumeister, W.4
Medalia, O.5
-
12
-
-
72349088728
-
Comparison of different methods for thin section EM analysis of Mycobacterium smegmatis
-
doi: 10.1111/j.1365-2818.2009.03299.x
-
Bleck CK, Merz A, Gutierrez MG, Walther P, Dubochet J, Zuber B, et al. 2010. Comparison of different methods for thin section EM analysis of Mycobacterium smegmatis. J Microsc 237:23-38. doi: 10.1111/j.1365-2818.2009.03299.x.
-
(2010)
J Microsc
, vol.237
, pp. 23-38
-
-
Bleck, C.K.1
Merz, A.2
Gutierrez, M.G.3
Walther, P.4
Dubochet, J.5
Zuber, B.6
-
13
-
-
3042812521
-
Structure and electrophysiological properties of the YscC secretin from the type III secretion system of Yersinia enterocolitica
-
doi: 10.1128/JB.186.14.4645-4654.2004
-
Burghout P, van Boxtel R, Van Gelder P, Ringler P, Muller SA, Tommassen J, et al. 2004. Structure and electrophysiological properties of the YscC secretin from the type III secretion system of Yersinia enterocolitica. J Bacteriol 186:4645-54. doi: 10.1128/JB.186.14.4645-4654.2004.
-
(2004)
J Bacteriol
, vol.186
, pp. 4645-4654
-
-
Burghout, P.1
van Boxtel, R.2
van Gelder, P.3
Ringler, P.4
Muller, S.A.5
Tommassen, J.6
-
14
-
-
84860574289
-
Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments
-
doi: 10.1016/j.jsb.2011.12.017
-
Castano-Diez D, Kudryashev M, Arheit M, Stahlberg H. 2012. Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J Struct Biol 178:139-51. doi: 10.1016/j.jsb.2011.12.017.
-
(2012)
J Struct Biol
, vol.178
, pp. 139-151
-
-
Castano-Diez, D.1
Kudryashev, M.2
Arheit, M.3
Stahlberg, H.4
-
15
-
-
79960620016
-
Structural diversity of bacterial flagellar motors
-
doi: 10.1038/emboj.2011.186
-
Chen S, Beeby M, Murphy GE, Leadbetter JR, Hendrixson DR, Briegel A, et al. 2011. Structural diversity of bacterial flagellar motors. EMBO J 30:2972-81. doi: 10.1038/emboj.2011.186.
-
(2011)
EMBO J
, vol.30
, pp. 2972-2981
-
-
Chen, S.1
Beeby, M.2
Murphy, G.E.3
Leadbetter, J.R.4
Hendrixson, D.R.5
Briegel, A.6
-
16
-
-
0028103275
-
The CCP4 suite: Programs for protein crystallography
-
Collaborative Computational Project, Number 4, doi: 10.1107/S0907444994003112
-
Collaborative Computational Project, Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760-3. doi: 10.1107/S0907444994003112.
-
(1994)
Acta Crystallogr D Biol Crystallogr
, vol.50
, pp. 760-763
-
-
-
17
-
-
33750110911
-
The type III secretion injectisome
-
doi: 10.1038/nrmicro1526
-
Cornelis GR. 2006. The type III secretion injectisome. Nat Rev Microbiol 4:811-25. doi: 10.1038/nrmicro1526.
-
(2006)
Nat Rev Microbiol
, vol.4
, pp. 811-825
-
-
Cornelis, G.R.1
-
18
-
-
0023255341
-
Transcription of the yop regulon from Y. enterocolitica requires trans acting pYV and chromosomal genes
-
doi: 10.1016/0882-4010(87)90078-7
-
Cornelis G, Vanootegem JC, Sluiters C. 1987. Transcription of the yop regulon from Y. enterocolitica requires trans acting pYV and chromosomal genes. Microb Pathog 2:367-79. doi: 10.1016/0882-4010(87)90078-7.
-
(1987)
Microb Pathog
, vol.2
, pp. 367-379
-
-
Cornelis, G.1
Vanootegem, J.C.2
Sluiters, C.3
-
19
-
-
15944376254
-
Structural and functional studies of the enteropathogenic Escherichia coli type III needle complex protein EscJ
-
doi: 10.1111/j.1365-2958.2005.04508.x
-
Crepin VF, Prasannan S, Shaw RK, Wilson RK, Creasey E, Abe CM, et al. 2005. Structural and functional studies of the enteropathogenic Escherichia coli type III needle complex protein EscJ. Mol Microbiol 55:1658-70. doi: 10.1111/j.1365-2958.2005.04508.x.
-
(2005)
Mol Microbiol
, vol.55
, pp. 1658-1670
-
-
Crepin, V.F.1
Prasannan, S.2
Shaw, R.K.3
Wilson, R.K.4
Creasey, E.5
Abe, C.M.6
-
20
-
-
0034142070
-
Novel approach to phasing proteins: Derivatization by short cryo-soaking with halides
-
doi: 10.1107/S0907444999016352
-
Dauter Z, Dauter M, Rajashankar KR. 2000. Novel approach to phasing proteins: derivatization by short cryo-soaking with halides. Acta Crystallogr D Biol Crystallogr 56:232-7. doi: 10.1107/S0907444999016352.
-
(2000)
Acta Crystallogr D Biol Crystallogr
, vol.56
, pp. 232-237
-
-
Dauter, Z.1
Dauter, M.2
Rajashankar, K.R.3
-
21
-
-
84879843809
-
Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling
-
doi: 10.1016/j.str.2013.05.014
-
Degiacomi M, Dal Peraro M. 2013. Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling. Structure 21:1097-1106. doi: 10.1016/j.str.2013.05.014.
-
(2013)
Structure
, vol.21
, pp. 1097-1106
-
-
Degiacomi, M.1
Dal Peraro, M.2
-
22
-
-
84884511250
-
Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism
-
doi: 10.1038/NCHEMBIO.1312
-
Degiacomi MT, Iacovache I, Pernot L, Chami M, Kudryashev M, Stahlberg H, et al. 2013. Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Nat Chem Biol. doi: 10.1038/NCHEMBIO.1312.
-
(2013)
Nat Chem Biol
-
-
Degiacomi, M.T.1
Iacovache, I.2
Pernot, L.3
Chami, M.4
Kudryashev, M.5
Stahlberg, H.6
-
23
-
-
77953123027
-
Deciphering the assembly of the Yersinia type III secretion injectisome
-
doi: 10.1038/emboj.2010.84
-
Diepold A, Amstutz M, Abel S, Sorg I, Jenal U, Cornelis GR. 2010. Deciphering the assembly of the Yersinia type III secretion injectisome. EMBO J 29:1928-40. doi: 10.1038/emboj.2010.84.
-
(2010)
EMBO J
, vol.29
, pp. 1928-1940
-
-
Diepold, A.1
Amstutz, M.2
Abel, S.3
Sorg, I.4
Jenal, U.5
Cornelis, G.R.6
-
24
-
-
79952468635
-
Bacterial nanomachines: The flagellum and type III injectisome
-
doi: 10.1101/cshperspect.a000299
-
Erhardt M, Namba K, Hughes KT. 2010. Bacterial nanomachines: the flagellum and type III injectisome. Cold Spring Harb perspect biol 2:a000299. doi: 10.1101/cshperspect.a000299.
-
(2010)
Cold Spring Harb Perspect Biol
, vol.2
-
-
Erhardt, M.1
Namba, K.2
Hughes, K.T.3
-
25
-
-
33750407288
-
Anisotropic network model: Systematic evaluation and a new web interface
-
doi: 10.1093/bioinformatics/btl448
-
Eyal E, Yang L-W, Bahar I. 2006. Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics 22:2619-27. doi: 10.1093/bioinformatics/btl448.
-
(2006)
Bioinformatics
, vol.22
, pp. 2619-2627
-
-
Eyal, E.1
Yang, L.-W.2
Bahar, I.3
-
26
-
-
0033810049
-
Modeling of loops in protein structures
-
doi: 10.1110/ps.9.9.1753
-
Fiser A, Do RKG, Šali A. 2000. Modeling of loops in protein structures. Protein Sci 9:1753-73. doi: 10.1110/ps.9.9.1753.
-
(2000)
Protein Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.G.2
Šali, A.3
-
27
-
-
0347383758
-
Modeller: Generation and refinement of homology-based protein structure models
-
doi: 10.1016/S0076-6879(03)74020-8
-
Fiser A, Sali A, Charles J, Carter W, Robert MS. 2003. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374:461-91. doi: 10.1016/S0076-6879(03)74020-8.
-
(2003)
Methods Enzymol
, vol.374
, pp. 461-491
-
-
Fiser, A.1
Sali, A.2
Charles, J.3
Carter, W.4
Robert, M.S.5
-
28
-
-
16344390563
-
Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography
-
doi: 10.1073/pnas.0409178102
-
Forster F, Medalia O, Zauberman N, Baumeister W, Fass D. 2005. Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc Natl Acad Sci USA 102:4729-34. doi: 10.1073/pnas.0409178102.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4729-4734
-
-
Forster, F.1
Medalia, O.2
Zauberman, N.3
Baumeister, W.4
Fass, D.5
-
29
-
-
84858633508
-
Structure of a type III secretion needle at 7-A resolution provides insights into its assembly and signaling mechanisms
-
doi: 10.1073/pnas.1116126109
-
Fujii T, Cheung M, Blanco A, Kato T, Blocker AJ, Namba K. 2012. Structure of a type III secretion needle at 7-A resolution provides insights into its assembly and signaling mechanisms. Proc Natl Acad Sci USA 109:4461-6. doi: 10.1073/pnas.1116126109.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 4461-4466
-
-
Fujii, T.1
Cheung, M.2
Blanco, A.3
Kato, T.4
Blocker, A.J.5
Namba, K.6
-
30
-
-
33845249292
-
Protein delivery into eukaryotic cells by type III secretion machines
-
doi: 10.1038/nature05272
-
Galan JE, Wolf-Watz H. 2006. Protein delivery into eukaryotic cells by type III secretion machines. Nature 444:567-73. doi: 10.1038/nature05272.
-
(2006)
Nature
, vol.444
, pp. 567-573
-
-
Galan, J.E.1
Wolf-Watz, H.2
-
31
-
-
23144457576
-
H++: A server for estimating pKas and adding missing hydrogens to macromolecules
-
doi: 10.1093/nar/gki464
-
Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A. 2005. H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33:368-71. doi: 10.1093/nar/gki464.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 368-371
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
Onufriev, A.6
-
32
-
-
66149119448
-
Three-dimensional reconstruction of the shigella T3SS transmembrane regions reveals 12-fold symmetry and novel features throughout
-
doi: 10.1038/nsmb.1599
-
Hodgkinson JL, Horsley A, Stabat D, Simon M, Johnson S, da Fonseca PC, et al. 2009. Three-dimensional reconstruction of the shigella T3SS transmembrane regions reveals 12-fold symmetry and novel features throughout. Nat Struct Mol Biol 16:477-85. doi: 10.1038/nsmb.1599.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 477-485
-
-
Hodgkinson, J.L.1
Horsley, A.2
Stabat, D.3
Simon, M.4
Johnson, S.5
da Fonseca, P.C.6
-
33
-
-
33645842748
-
Genome characterization of a flexuous rod-shaped mycovirus, botrytis virus X, reveals high amino acid identity to genes from plant 'potex-like' viruses
-
doi: 10.1007/s00705-005-0621-y
-
Howitt RL, Beever RE, Pearson MN, Forster RL. 2006. Genome characterization of a flexuous rod-shaped mycovirus, botrytis virus X, reveals high amino acid identity to genes from plant 'potex-like' viruses. Arch virol 151:563-79. doi: 10.1007/s00705-005-0621-y.
-
(2006)
Arch Virol
, vol.151
, pp. 563-579
-
-
Howitt, R.L.1
Beever, R.E.2
Pearson, M.N.3
Forster, R.L.4
-
34
-
-
79951821839
-
Improved resolution of tertiary structure elasticity in muscle protein
-
doi: 10.1016/j.bpj.2011.01.019
-
Hsin J, Schulten K. 2011. Improved resolution of tertiary structure elasticity in muscle protein. Biophys J 100:L22-4. doi: 10.1016/j.bpj.2011.01.019.
-
(2011)
Biophys J
, vol.100
-
-
Hsin, J.1
Schulten, K.2
-
35
-
-
0029878720
-
VMD: Visual molecular dynamics
-
doi: 10.1016/0263-7855(96)00018-5
-
Humphrey W, Dalke A, Schulten K. 1996. VMD: visual molecular dynamics. J Mol Graph 14:33-8. doi: 10.1016/0263-7855(96)00018-5.
-
(1996)
J Mol Graph
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
36
-
-
34247493236
-
Matplotlib: A 2D graphics environment
-
Hunter JD. 2007. Matplotlib: a 2D graphics environment. In: Computing in science and engineering. p. 90-5. doi: 10.1109/MCSE.2007.55.
-
(2007)
Computing In Science and Engineering
, pp. 90-95
-
-
Hunter, J.D.1
-
37
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
doi: 10.1063/1.445869
-
Jorgensen WL, Chandrasekhar J, Madura J, Klein ML. 1983. Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926. doi: 10.1063/1.445869.
-
(1983)
J Chem Phys
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Klein, M.L.4
-
38
-
-
76449106188
-
Integration, scaling, space-group assignment and post-refinement
-
doi: 10.1107/S0907444909047374
-
Kabsch W. 2010a. Integration, scaling, space-group assignment and post-refinement. Acta Cryst Sect D Biol Crystallogr 66:133-44. doi: 10.1107/S0907444909047374.
-
(2010)
Acta Cryst Sect D Biol Crystallogr
, vol.66
, pp. 133-144
-
-
Kabsch, W.1
-
40
-
-
0025837193
-
A wide-host-range suicide vector for improving reverse genetics in gram-negative bacteria: Inactivation of the blaA gene of Yersinia enterocolitica
-
doi: 10.1016/0378-1119(91)90599-7
-
Kaniga K, Delor I, Cornelis GR. 1991. A wide-host-range suicide vector for improving reverse genetics in gram-negative bacteria: inactivation of the blaA gene of Yersinia enterocolitica. Gene 109:137-41. doi: 10.1016/0378-1119(91)90599-7.
-
(1991)
Gene
, vol.109
, pp. 137-141
-
-
Kaniga, K.1
Delor, I.2
Cornelis, G.R.3
-
41
-
-
0034718542
-
Contribution of Salmonella typhimurium type III secretion components to needle complex formation
-
doi: 10.1073/pnas.200209497
-
Kimbrough TG, Miller SI. 2000. Contribution of Salmonella typhimurium type III secretion components to needle complex formation. Proc Natl Acad Sci USA 97:11008-13. doi: 10.1073/pnas.200209497.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 11008-11013
-
-
Kimbrough, T.G.1
Miller, S.I.2
-
42
-
-
85010292860
-
The biophysics of the gram-negative periplasmic space
-
doi: 10.1080/10408419891294172
-
Koch AL. 1998. The biophysics of the gram-negative periplasmic space. Crit Rev Microbiol 24:23-59. doi: 10.1080/10408419891294172.
-
(1998)
Crit Rev Microbiol
, vol.24
, pp. 23-59
-
-
Koch, A.L.1
-
43
-
-
0029879295
-
Computer visualization of three-dimensional image data using IMOD
-
doi: 10.1006/jsbi.1996.0013
-
Kremer JR, Mastronarde DN, McIntosh JR. 1996. Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116:71-6. doi: 10.1006/jsbi.1996.0013.
-
(1996)
J Struct Biol
, vol.116
, pp. 71-76
-
-
Kremer, J.R.1
Mastronarde, D.N.2
McIntosh, J.R.3
-
44
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
doi: 10.1107/S0907444904026460
-
Krissinel E, Henrick K. 2004. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60:2256-68. doi: 10.1107/S0907444904026460.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
45
-
-
84887220667
-
Limiting factors in single particle cryo electron tomography
-
doi: 10.5936/csbj.201207002
-
Kudryashev M, Castano-Diez D, Stahlberg H. 2012a. Limiting factors in single particle cryo electron tomography. Comput Struct Biotechnol J 1:e201207002. doi: 10.5936/csbj.201207002.
-
(2012)
Comput Struct Biotechnol J
, vol.1
-
-
Kudryashev, M.1
Castano-Diez, D.2
Stahlberg, H.3
-
46
-
-
72449145288
-
Distinct in situ structures of the Borrelia flagellar motor
-
doi: 10.1016/j.jsb.2009.08.008
-
Kudryashev M, Cyrklaff M, Wallich R, Baumeister W, Frischknecht F. 2010. Distinct in situ structures of the Borrelia flagellar motor. J Struct Biol 169:54-61. doi: 10.1016/j.jsb.2009.08.008.
-
(2010)
J Struct Biol
, vol.169
, pp. 54-61
-
-
Kudryashev, M.1
Cyrklaff, M.2
Wallich, R.3
Baumeister, W.4
Frischknecht, F.5
-
47
-
-
84860590097
-
Assessing the benefits of focal pair cryo-electron tomography
-
doi: 10.1016/j.jsb.2011.10.004
-
Kudryashev M, Stahlberg H, Castano-Diez D. 2012b. Assessing the benefits of focal pair cryo-electron tomography. J Struct Biol 178:88-97. doi: 10.1016/j.jsb.2011.10.004.
-
(2012)
J Struct Biol
, vol.178
, pp. 88-97
-
-
Kudryashev, M.1
Stahlberg, H.2
Castano-Diez, D.3
-
48
-
-
84857134729
-
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach
-
doi: 10.1073/pnas.1120559109
-
Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, et al. 2012. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA 109:1380-7. doi: 10.1073/pnas.1120559109.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 1380-1387
-
-
Lasker, K.1
Forster, F.2
Bohn, S.3
Walzthoeni, T.4
Villa, E.5
Unverdorben, P.6
-
49
-
-
77953161216
-
A conserved domain in type III secretion links the cytoplasmic domain of InvA to elements of the basal body
-
doi: 10.1107/S0907444910010796
-
Lilic M, Quezada CM, Stebbins CE. 2010. A conserved domain in type III secretion links the cytoplasmic domain of InvA to elements of the basal body. Acta Cryst Sect D Biol Crystallogr 66:709-13. doi: 10.1107/S0907444910010796.
-
(2010)
Acta Cryst Sect D Biol Crystallogr
, vol.66
, pp. 709-713
-
-
Lilic, M.1
Quezada, C.M.2
Stebbins, C.E.3
-
50
-
-
80051941010
-
Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli
-
doi: 10.1016/j.virol.2011.06.005
-
Liu J, Chen CY, Shiomi D, Niki H, Margolin W. 2011. Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli. Virology 417:304-11. doi: 10.1016/j.virol.2011.06.005.
-
(2011)
Virology
, vol.417
, pp. 304-311
-
-
Liu, J.1
Chen, C.Y.2
Shiomi, D.3
Niki, H.4
Margolin, W.5
-
51
-
-
67749093018
-
Intact flagellar motor of Borrelia burgdorferi revealed by cryo-electron tomography: Evidence for stator ring curvature and rotor/C-ring assembly flexion
-
doi: 10.1128/JB.00340-09
-
Liu J, Lin T, Botkin DJ, McCrum E, Winkler H, Norris SJ. 2009. Intact flagellar motor of Borrelia burgdorferi revealed by cryo-electron tomography: evidence for stator ring curvature and rotor/C-ring assembly flexion. J Bacteriol 191:5026-36. doi: 10.1128/JB.00340-09.
-
(2009)
J Bacteriol
, vol.191
, pp. 5026-5036
-
-
Liu, J.1
Lin, T.2
Botkin, D.J.3
McCrum, E.4
Winkler, H.5
Norris, S.J.6
-
52
-
-
84862270506
-
Atomic model of the type III secretion system needle
-
doi: 10.1038/nature11079
-
Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, et al. 2012. Atomic model of the type III secretion system needle. Nature 486:276-9. doi: 10.1038/nature11079.
-
(2012)
Nature
, vol.486
, pp. 276-279
-
-
Loquet, A.1
Sgourakis, N.G.2
Gupta, R.3
Giller, K.4
Riedel, D.5
Goosmann, C.6
-
53
-
-
84857828509
-
Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system
-
doi: 10.1107/S0907444911054308
-
Lountos GT, Tropea JE, Waugh DS. 2012. Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system. Acta Cryst Sect D Biol Crystallogr 68:201-9. doi: 10.1107/S0907444911054308.
-
(2012)
Acta Cryst Sect D Biol Crystallogr
, vol.68
, pp. 201-209
-
-
Lountos, G.T.1
Tropea, J.E.2
Waugh, D.S.3
-
54
-
-
0041784950
-
All-atom Empirical potential for molecular modeling and dynamics studies of proteins
-
doi: 10.1021/jp973084f
-
MacKerell AD, Bashford D, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, et al. 1998. All-atom Empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-616. doi: 10.1021/jp973084f.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Dunbrack, R.L.3
Evanseck, J.D.4
Field, M.J.5
Fischer, S.6
-
55
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
doi: 10.1002/jcc.20065
-
Mackerell AD, Feig M, Brooks CL. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comp Chem 25:1400-15. doi: 10.1002/jcc.20065.
-
(2004)
J Comp Chem
, vol.25
, pp. 1400-1415
-
-
Mackerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
56
-
-
8344258355
-
Structural insights into the assembly of the type III secretion needle complex
-
doi: 10.1126/science.1102610
-
Marlovits TC, Kubori T, Sukhan A, Thomas DR, Galan JE, Unger VM. 2004. Structural insights into the assembly of the type III secretion needle complex. Science 306:1040-2. doi: 10.1126/science.1102610.
-
(2004)
Science
, vol.306
, pp. 1040-1042
-
-
Marlovits, T.C.1
Kubori, T.2
Sukhan, A.3
Thomas, D.R.4
Galan, J.E.5
Unger, V.M.6
-
57
-
-
34447508216
-
Phaser crystallographic software
-
doi: 10.1107/S0021889807021206
-
Mccoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. 2007. Phaser crystallographic software. J Appl Crystallogr 40:658-74. doi: 10.1107/S0021889807021206.
-
(2007)
J Appl Crystallogr
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
58
-
-
0347383760
-
ARP/wARP and automatic interpretation of protein electron density maps
-
doi: 10.1016/S0076-6879(03)74011-7
-
Morris RJ, Perrakis A, Lamzin VS. 2003. ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol 374:229-44. doi: 10.1016/S0076-6879(03)74011-7.
-
(2003)
Methods Enzymol
, vol.374
, pp. 229-244
-
-
Morris, R.J.1
Perrakis, A.2
Lamzin, V.S.3
-
59
-
-
58149347646
-
Mechanisms of type III protein export for bacterial flagellar assembly
-
doi: 10.1039/b808065h
-
Minamino T, Imada K, Namba K. 2008. Mechanisms of type III protein export for bacterial flagellar assembly. Mol Biosyst 4:1105-15. doi: 10.1039/b808065h.
-
(2008)
Mol Biosyst
, vol.4
, pp. 1105-1115
-
-
Minamino, T.1
Imada, K.2
Namba, K.3
-
60
-
-
33644860766
-
Shigella Spa33 is an essential C-ring component of type III secretion machinery
-
doi: 10.1074/jbc.M509644200
-
Morita-Ishihara T, Ogawa M, Sagara H, Yoshida M, Katayama E, Sasakawa C. 2006. Shigella Spa33 is an essential C-ring component of type III secretion machinery. J Biol Chem 281:599-607. doi: 10.1074/jbc.M509644200.
-
(2006)
J Biol Chem
, vol.281
, pp. 599-607
-
-
Morita-Ishihara, T.1
Ogawa, M.2
Sagara, H.3
Yoshida, M.4
Katayama, E.5
Sasakawa, C.6
-
61
-
-
0030924992
-
Refinement of macromolecular structures by the maximum-likelihood method
-
doi: 10.1107/S0907444996012255
-
Murshudov GN, Vagin AA, Dodson EJ. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst Sect D Biol Crystallogr 53:240-55. doi: 10.1107/S0907444996012255.
-
(1997)
Acta Cryst Sect D Biol Crystallogr
, vol.53
, pp. 240-255
-
-
Murshudov, G.N.1
Vagin, A.A.2
Dodson, E.J.3
-
62
-
-
84879650647
-
A novel effector secretion mechanism based on proton-motive force-dependent type III secretion apparatus rotation
-
doi: 10.1096/fj.13-229054
-
Ohgita T, Hayashi N, Hama S, Tsuchiya H, Gotoh N, Kogure K. 2013. A novel effector secretion mechanism based on proton-motive force-dependent type III secretion apparatus rotation. FASEB J 27:2862-72. doi: 10.1096/fj.13-229054.
-
(2013)
FASEB J
, vol.27
, pp. 2862-2872
-
-
Ohgita, T.1
Hayashi, N.2
Hama, S.3
Tsuchiya, H.4
Gotoh, N.5
Kogure, K.6
-
63
-
-
15944409588
-
Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: A Darwinian perspective
-
doi: 10.1016/j.femsre.2005.01.001
-
Pallen MJ, Beatson SA, Bailey CM. 2005. Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective. FEMS Microbiol Rev 29:201-29. doi: 10.1016/j.femsre.2005.01.001.
-
(2005)
FEMS Microbiol Rev
, vol.29
, pp. 201-229
-
-
Pallen, M.J.1
Beatson, S.A.2
Bailey, C.M.3
-
64
-
-
70349602499
-
On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination
-
doi: 10.1107/S0907444909029643
-
Panjikar S, Parthasarathy V, Lamzin VS, Weiss MS, Tucker PA. 2009. On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination. Acta Crystallogr D Biol Crystallogr 65:1089-97. doi: 10.1107/S0907444909029643.
-
(2009)
Acta Crystallogr D Biol Crystallogr
, vol.65
, pp. 1089-1097
-
-
Panjikar, S.1
Parthasarathy, V.2
Lamzin, V.S.3
Weiss, M.S.4
Tucker, P.A.5
-
65
-
-
80054030401
-
Oxidative doping renders graphene hydrophilic, facilitating its use as a support in biological TEM
-
doi: 10.1021/nl202386p
-
Pantelic RS, Suk JW, Hao Y, Ruoff RS, Stahlberg H. 2011. Oxidative doping renders graphene hydrophilic, facilitating its use as a support in biological TEM. Nano Lett 11:4319-23. doi: 10.1021/nl202386p.
-
(2011)
Nano Lett
, vol.11
, pp. 4319-4323
-
-
Pantelic, R.S.1
Suk, J.W.2
Hao, Y.3
Ruoff, R.S.4
Stahlberg, H.5
-
66
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
doi: 10.1002/jcc.20289
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. 2005. Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-802. doi: 10.1002/jcc.20289.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
-
67
-
-
16644397843
-
Developments in the CCP4 molecular-graphics project
-
doi: 10.1107/S0907444904023716
-
Potterton L, McNicholas S, Krissinel E, Gruber J, Cowtan K, Emsley P, et al. 2004. Developments in the CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr 60:2288-94. doi: 10.1107/S0907444904023716.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, pp. 2288-2294
-
-
Potterton, L.1
McNicholas, S.2
Krissinel, E.3
Gruber, J.4
Cowtan, K.5
Emsley, P.6
-
68
-
-
79955529365
-
A C-terminal region of Yersinia pestis YscD binds the outer membrane secretin YscC
-
doi: 10.1128/JB.01137-10
-
Ross JA, Plano GV. 2011. A C-terminal region of Yersinia pestis YscD binds the outer membrane secretin YscC. J Bacteriol 193:2276-89. doi: 10.1128/JB.01137-10.
-
(2011)
J Bacteriol
, vol.193
, pp. 2276-2289
-
-
Ross, J.A.1
Plano, G.V.2
-
69
-
-
79551681054
-
Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system
-
doi: 10.1128/mBio.00158-10
-
Sanowar S, Singh P, Pfuetzner RA, Andre I, Zheng H, Spreter T, et al. 2010. Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system. MBio 1:e00158-10. doi: 10.1128/mBio.00158-10.
-
(2010)
MBio
, vol.1
-
-
Sanowar, S.1
Singh, P.2
Pfuetzner, R.A.3
Andre, I.4
Zheng, H.5
Spreter, T.6
-
70
-
-
0026035531
-
Genetic and molecular basis of epithelial cell invasion by Shigella species
-
doi: 0162-0886/91/1302-0044$02.00
-
Sansonetti PJ. 1991. Genetic and molecular basis of epithelial cell invasion by Shigella species. Rev Infect Dis 13(Suppl 4):S285-92. doi: 0162-0886/91/1302-0044$02.00.
-
(1991)
Rev Infect Dis
, vol.13
, Issue.4 SUPPL.
-
-
Sansonetti, P.J.1
-
71
-
-
84866078359
-
Prevention of overfitting in cryo-EM structure determination
-
doi: 10.1038/nmeth.2115
-
Scheres SH, Chen S. 2012. Prevention of overfitting in cryo-EM structure determination. Nat Methods 9:853-4. doi: 10.1038/nmeth.2115.
-
(2012)
Nat Methods
, vol.9
, pp. 853-854
-
-
Scheres, S.H.1
Chen, S.2
-
72
-
-
77954067915
-
Topology and organization of the Salmonella typhimurium type III secretion needle complex components
-
doi: 10.1371/journal.ppat.1000824
-
Schraidt O, Lefebre MD, Brunner MJ, Schmied WH, Schmidt A, Radics J, et al. 2010. Topology and organization of the Salmonella typhimurium type III secretion needle complex components. PLOS Pathog 6:e1000824. doi: 10.1371/journal.ppat.1000824.
-
(2010)
PLOS Pathog
, vol.6
-
-
Schraidt, O.1
Lefebre, M.D.2
Brunner, M.J.3
Schmied, W.H.4
Schmidt, A.5
Radics, J.6
-
73
-
-
79952262440
-
Three-dimensional model of Salmonella's needle complex at subnanometer resolution
-
doi: 10.1126/science.1199358
-
Schraidt O, Marlovits TC. 2011. Three-dimensional model of Salmonella's needle complex at subnanometer resolution. Science 331:1192-5. doi: 10.1126/science.1199358.
-
(2011)
Science
, vol.331
, pp. 1192-1195
-
-
Schraidt, O.1
Marlovits, T.C.2
-
74
-
-
39749175060
-
Membrane localization and topology of the Yersinia pestis YscJ lipoprotein
-
doi: 10.1099/mic.0.2007/013045-0
-
Silva-Herzog E, Ferracci F, Jackson MW, Joseph SS, Plano GV. 2008. Membrane localization and topology of the Yersinia pestis YscJ lipoprotein. Microbiology 154:593-607. doi: 10.1099/mic.0.2007/013045-0.
-
(2008)
Microbiology
, vol.154
, pp. 593-607
-
-
Silva-Herzog, E.1
Ferracci, F.2
Jackson, M.W.3
Joseph, S.S.4
Plano, G.V.5
-
75
-
-
0029608720
-
Identification of the YopE and YopH domains required for secretion and internalization into the cytosol of macrophages, using the cyaA gene fusion approach
-
doi: 10.1073/pnas.92.26.11998
-
Sory MP, Boland A, Lambermont I, Cornelis GR. 1995. Identification of the YopE and YopH domains required for secretion and internalization into the cytosol of macrophages, using the cyaA gene fusion approach. Proc Natl Acad Sci USA 92:11998-2002. doi: 10.1073/pnas.92.26.11998.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 11998-12002
-
-
Sory, M.P.1
Boland, A.2
Lambermont, I.3
Cornelis, G.R.4
-
76
-
-
66149092022
-
A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system
-
doi: 10.1038/nsmb.1603
-
Spreter T, Yip CK, Sanowar S, Andre I, Kimbrough TG, Vuckovic M, et al. 2009. A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nat Struct Mol Biol 16:468-76. doi: 10.1038/nsmb.1603.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 468-476
-
-
Spreter, T.1
Yip, C.K.2
Sanowar, S.3
Andre, I.4
Kimbrough, T.G.5
Vuckovic, M.6
-
77
-
-
79956211337
-
Identification of small-molecule inhibitors of Yersinia pestis Type III secretion system YscN ATPase
-
doi: 10.1371/journal. pone.0019716
-
Swietnicki W, Carmany D, Retford M, Guelta M, Dorsey R, Bozue J, et al. 2011. Identification of small-molecule inhibitors of Yersinia pestis Type III secretion system YscN ATPase. PLOS ONE 6:e19716. doi: 10.1371/journal. pone.0019716.
-
(2011)
PLOS ONE
, vol.6
-
-
Swietnicki, W.1
Carmany, D.2
Retford, M.3
Guelta, M.4
Dorsey, R.5
Bozue, J.6
-
78
-
-
26844521751
-
Type III secretion: More systems than you think
-
doi: 10.1152/physiol.00011.2005
-
Troisfontaines P, Cornelis GR. 2005. Type III secretion: more systems than you think. Physiology (Bethesda) 20:326-39. doi: 10.1152/physiol.00011.2005.
-
(2005)
Physiology (Bethesda)
, vol.20
, pp. 326-339
-
-
Troisfontaines, P.1
Cornelis, G.R.2
-
79
-
-
25144494651
-
Fourier shell correlation threshold criteria
-
doi: 10.1016/j. jsb.2005.05.009
-
van Heel M, Schatz M. 2005. Fourier shell correlation threshold criteria. J Struct Biol 151:250-62. doi: 10.1016/j. jsb.2005.05.009.
-
(2005)
J Struct Biol
, vol.151
, pp. 250-262
-
-
van Heel, M.1
Schatz, M.2
-
80
-
-
84867910247
-
3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography
-
doi: 10.1016/j.jsb.2012.07.003
-
Wang K, Strunk K, Zhao G, Gray JL, Zhang P. 2012. 3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography. J Struct Biol 180:318-26. doi: 10.1016/j.jsb.2012.07.003.
-
(2012)
J Struct Biol
, vol.180
, pp. 318-326
-
-
Wang, K.1
Strunk, K.2
Zhao, G.3
Gray, J.L.4
Zhang, P.5
-
81
-
-
79551685139
-
Structural overview of the bacterial injectisome
-
doi: 10.1016/j.mib.2010.10.009
-
Worrall LJ, Lameignere E, Strynadka NC. 2011. Structural overview of the bacterial injectisome. Curr Opin Microbiol 14:3-8. doi: 10.1016/j.mib.2010.10.009.
-
(2011)
Curr Opin Microbiol
, vol.14
, pp. 3-8
-
-
Worrall, L.J.1
Lameignere, E.2
Strynadka, N.C.3
-
82
-
-
20444488138
-
Structural characterization of the molecular platform for type III secretion system assembly
-
doi: 10.1038/nature03554
-
Yip CK, Kimbrough TG, Felise HB, Vuckovic M, Thomas NA, Pfuetzner RA, et al. 2005. Structural characterization of the molecular platform for type III secretion system assembly. Nature 435:702-7. doi: 10.1038/nature03554.
-
(2005)
Nature
, vol.435
, pp. 702-707
-
-
Yip, C.K.1
Kimbrough, T.G.2
Felise, H.B.3
Vuckovic, M.4
Thomas, N.A.5
Pfuetzner, R.A.6
|