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Volumn 6, Issue , 2017, Pages

Model-based local density sharpening of cryo-EM maps

Author keywords

[No Author keywords available]

Indexed keywords

BETA GALACTOSIDASE; DNA DIRECTED RNA POLYMERASE III; GAMMA SECRETASE; ISOPROPYL THIOGALACTOSIDE; PROTEASOME; TRYPTOPHAN; VANILLOID RECEPTOR 1;

EID: 85036517329     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.27131     Document Type: Article
Times cited : (163)

References (71)
  • 2
    • 0021257186 scopus 로고
    • Cryo-electron microscopy of viruses
    • Adrian M, Dubochet J, Lepault J, McDowall AW. 1984. Cryo-electron microscopy of viruses. Nature 308:32-36. DOI:https://doi.org/10.1038/308032a0
    • (1984) Nature , vol.308 , pp. 32-36
    • Adrian, M.1    Dubochet, J.2    Lepault, J.3    McDowall, A.W.4
  • 4
    • 0006908476 scopus 로고
    • Method for obtaining a high resolution protein map starting from a low resolution map
    • Agarwal RC, Isaacs NW. 1977. Method for obtaining a high resolution protein map starting from a low resolution map. PNAS 74:2835-2839. DOI:https://doi.org/10.1073/pnas.74.7.2835
    • (1977) PNAS , vol.74 , pp. 2835-2839
    • Agarwal, R.C.1    Isaacs, N.W.2
  • 5
    • 84898761737 scopus 로고    scopus 로고
    • Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector
    • Allegretti M, Mills DJ, McMullan G, Kühlbrandt W, Vonck J. 2014. Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector. eLife 3:e01963. DOI:https://doi.org/10.7554/eLife.01963
    • (2014) eLife , vol.3
    • Allegretti, M.1    Mills, D.J.2    McMullan, G.3    Kühlbrandt, W.4    Vonck, J.5
  • 7
    • 84878580683 scopus 로고    scopus 로고
    • Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles
    • Bai XC, Fernandez IS, McMullan G, Scheres SH. 2013. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife 2:e00461. DOI:https://doi.org/10.7554/eLife.00461
    • (2013) eLife , vol.2
    • Bai, X.C.1    Fernandez, I.S.2    McMullan, G.3    Scheres, S.H.4
  • 9
    • 84959080555 scopus 로고    scopus 로고
    • EMRinger: Side chain-directed model and map validation for 3D cryo-electron microscopy
    • Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS. 2015. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nature Methods 12:943-946. DOI:https://doi.org/10.1038/nmeth.3541
    • (2015) Nature Methods , vol.12 , pp. 943-946
    • Barad, B.A.1    Echols, N.2    Wang, R.Y.3    Cheng, Y.4    DiMaio, F.5    Adams, P.D.6    Fraser, J.S.7
  • 10
    • 84930667920 scopus 로고    scopus 로고
    • 2.2 A° resolution cryo-EM structure of b-galactosidase in complex with a cell-permeant inhibitor
    • Bartesaghi A, Merk A, Banerjee S, Matthies D, Wu X, Milne JL, Subramaniam S. 2015. 2.2 A° resolution cryo-EM structure of b-galactosidase in complex with a cell-permeant inhibitor. Science 348:1147-1151. DOI:https://doi.org/10.1126/science.aab1576
    • (2015) Science , vol.348 , pp. 1147-1151
    • Bartesaghi, A.1    Merk, A.2    Banerjee, S.3    Matthies, D.4    Wu, X.5    Milne, J.L.6    Subramaniam, S.7
  • 15
    • 84924617498 scopus 로고    scopus 로고
    • 2.8 A° resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy
    • Campbell MG, Veesler D, Cheng A, Potter CS, Carragher B. 2015. 2.8 A° resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. eLife 4:e06380. DOI:https://doi.org/10.7554/eLife.06380
    • (2015) eLife , vol.4
    • Campbell, M.G.1    Veesler, D.2    Cheng, A.3    Potter, C.S.4    Carragher, B.5
  • 16
    • 84887242753 scopus 로고    scopus 로고
    • One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions
    • Cardone G, Heymann JB, Steven AC. 2013. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. Journal of Structural Biology 184:226-236. DOI:https://doi.org/10.1016/j.jsb.2013.08.002
    • (2013) Journal of Structural Biology , vol.184 , pp. 226-236
    • Cardone, G.1    Heymann, J.B.2    Steven, A.C.3
  • 18
    • 84928400353 scopus 로고    scopus 로고
    • Single-particle cryo-EM at crystallographic resolution
    • Cheng Y. 2015. Single-particle cryo-EM at crystallographic resolution. Cell 161:450-457. DOI:https://doi.org/10.1016/j.cell.2015.03.049
    • (2015) Cell , vol.161 , pp. 450-457
    • Cheng, Y.1
  • 21
  • 22
    • 0141507032 scopus 로고    scopus 로고
    • Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains
    • DeLaBarre B, Brunger AT. 2003. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nature Structural & Molecular Biology 10:856-863. DOI:https://doi.org/10.1038/nsb972
    • (2003) Nature Structural & Molecular Biology , vol.10 , pp. 856-863
    • DeLaBarre, B.1    Brunger, A.T.2
  • 25
    • 0008865745 scopus 로고
    • Fourier transform of an electron micrograph: Effects of defocussing and aberrations, and implications for the use of underfocus contrast enhancement
    • Erickson HP, Klug A. 1970. Fourier transform of an electron micrograph: effects of defocussing and aberrations, and implications for the use of underfocus contrast enhancement. Bericht Bunsen Gesell 74:1129-1137. DOI:https://doi.org/10.1002/bbpc.19700741109
    • (1970) Bericht Bunsen Gesell , vol.74 , pp. 1129-1137
    • Erickson, H.P.1    Klug, A.2
  • 26
    • 19844377583 scopus 로고    scopus 로고
    • The 13 angstroms structure of a chaperonin GroEL- protein substrate complex by cryo-electron microscopy
    • Falke S, Tama F, Brooks CL, Gogol EP, Fisher MT. 2005. The 13 angstroms structure of a chaperonin GroEL- protein substrate complex by cryo-electron microscopy. Journal of Molecular Biology 348:219-230. DOI:https://doi.org/10.1016/j.jmb.2005.02.027
    • (2005) Journal of Molecular Biology , vol.348 , pp. 219-230
    • Falke, S.1    Tama, F.2    Brooks, C.L.3    Gogol, E.P.4    Fisher, M.T.5
  • 27
    • 35549001684 scopus 로고    scopus 로고
    • Electronic detectors for electron microscopy
    • Faruqi AR, Henderson R. 2007. Electronic detectors for electron microscopy. Current Opinion in Structural Biology 17:549-555. DOI:https://doi.org/10.1016/j.sbi.2007.08.014
    • (2007) Current Opinion in Structural Biology , vol.17 , pp. 549-555
    • Faruqi, A.R.1    Henderson, R.2
  • 29
    • 84928560614 scopus 로고    scopus 로고
    • Structure of the E. Coli ribosome-EF-Tu complex at <3 A° resolution by Cs-corrected cryo-EM
    • Fischer N, Neumann P, Konevega AL, Bock LV, Ficner R, Rodnina MV, Stark H. 2015. Structure of the E. coli ribosome-EF-Tu complex at <3 A° resolution by Cs-corrected cryo-EM. Nature 520:567-570. DOI:https://doi.org/10.1038/nature14275
    • (2015) Nature , vol.520 , pp. 567-570
    • Fischer, N.1    Neumann, P.2    Konevega, A.L.3    Bock, L.V.4    Ficner, R.5    Rodnina, M.V.6    Stark, H.7
  • 33
    • 0036111645 scopus 로고    scopus 로고
    • The computational crystallography toolbox: Crystallographic algorithms in a reusable software framework
    • Grosse-Kunstleve RW, Sauter NK, Moriarty NW, Adams PD. 2002. The computational crystallography toolbox: crystallographic algorithms in a reusable software framework. Journal of Applied Crystallography 35:126-136. DOI:https://doi.org/10.1107/S0021889801017824
    • (2002) Journal of Applied Crystallography , vol.35 , pp. 126-136
    • Grosse-Kunstleve, R.W.1    Sauter, N.K.2    Moriarty, N.W.3    Adams, P.D.4
  • 34
    • 0000313739 scopus 로고
    • Exact filters for general geometry three dimensional reconstruction
    • Harauz G, van Heel M. 1986. Exact filters for general geometry three dimensional reconstruction. Optik 73:146-156.
    • (1986) Optik , vol.73 , pp. 146-156
    • Harauz, G.1    van Heel, M.2
  • 35
    • 0026523919 scopus 로고
    • Image contrast in high-resolution electron microscopy of biological macromolecules: TMV in ice
    • Henderson R. 1992. Image contrast in high-resolution electron microscopy of biological macromolecules: TMV in ice. Ultramicroscopy 46:1-18. DOI:https://doi.org/10.1016/0304-3991(92)90003-3
    • (1992) Ultramicroscopy , vol.46 , pp. 1-18
    • Henderson, R.1
  • 38
    • 0001041450 scopus 로고
    • The crystal and molecular structure of cellobiose
    • Jacobson RA, Wunderlich JA, Lipscomb WN. 1961. The crystal and molecular structure of cellobiose. Acta Crystallographica 14:598-607. DOI:https://doi.org/10.1107/S0365110X61001893
    • (1961) Acta Crystallographica , vol.14 , pp. 598-607
    • Jacobson, R.A.1    Wunderlich, J.A.2    Lipscomb, W.N.3
  • 40
    • 0028172551 scopus 로고
    • Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures
    • Jiang JS, Brunger AT. 1994. Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures. Journal of Molecular Biology 243:100-115. DOI:https://doi.org/10.1006/jmbi.1994.1633
    • (1994) Journal of Molecular Biology , vol.243 , pp. 100-115
    • Jiang, J.S.1    Brunger, A.T.2
  • 41
    • 85009064131 scopus 로고    scopus 로고
    • Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images
    • Jonić S. 2017. Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images. Current Opinion in Structural Biology 43:114-121. DOI:https://doi.org/10.1016/j.sbi.2016.12.011
    • (2017) Current Opinion in Structural Biology , vol.43 , pp. 114-121
    • Jonić, S.1
  • 42
    • 84961233652 scopus 로고    scopus 로고
    • Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment
    • Joseph AP, Malhotra S, Burnley T, Wood C, Clare DK, Winn M, Topf M. 2016. Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. Methods 100:42-49. DOI:https://doi.org/10.1016/j.ymeth.2016.03.007
    • (2016) Methods , vol.100 , pp. 42-49
    • Joseph, A.P.1    Malhotra, S.2    Burnley, T.3    Wood, C.4    Clare, D.K.5    Winn, M.6    Topf, M.7
  • 43
    • 84897000286 scopus 로고    scopus 로고
    • The resolution revolution
    • Kuhlbrandt W. 2014. The resolution revolution. Science 343:1443-1444. DOI:https://doi.org/10.1126/science.1251652
    • (2014) Science , vol.343 , pp. 1443-1444
    • Kuhlbrandt, W.1
  • 44
    • 84889607320 scopus 로고    scopus 로고
    • Structure of the TRPV1 ion channel determined by electron cryo-microscopy
    • Liao M, Cao E, Julius D, Cheng Y. 2013. Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:107-112. DOI:https://doi.org/10.1038/nature12822
    • (2013) Nature , vol.504 , pp. 107-112
    • Liao, M.1    Cao, E.2    Julius, D.3    Cheng, Y.4
  • 46
  • 52
    • 84977542628 scopus 로고    scopus 로고
    • Refinement of atomic structures against cryo-EM maps
    • Murshudov GN. 2016. Refinement of atomic structures against cryo-EM maps. Methods in Enzymology 579:277-305. DOI:https://doi.org/10.1016/bs.mie.2016.05.033
    • (2016) Methods in Enzymology , vol.579 , pp. 277-305
    • Murshudov, G.N.1
  • 53
    • 33646260450 scopus 로고    scopus 로고
    • Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    • Painter J, Merritt EA. 2006. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallographica. Section D, Biological Crystallography 62:439-450. DOI:https://doi.org/10.1107/S0907444906005270
    • (2006) Acta Crystallographica. Section D, Biological Crystallography , vol.62 , pp. 439-450
    • Painter, J.1    Merritt, E.A.2
  • 55
    • 84944812409 scopus 로고
    • Improved Fourier coefficients for maps using phases from partial structures with errors
    • Read RJ. 1986. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallographica. Section A, Foundations of Crystallography 42:140-149. DOI:https://doi.org/10.1107/S0108767386099622
    • (1986) Acta Crystallographica. Section A, Foundations of Crystallography , vol.42 , pp. 140-149
    • Read, R.J.1
  • 56
    • 0142042865 scopus 로고    scopus 로고
    • Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy
    • Rosenthal PB, Henderson R. 2003. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology 333:721-745. DOI:https://doi.org/10.1016/j.jmb.2003.07.013
    • (2003) Journal of Molecular Biology , vol.333 , pp. 721-745
    • Rosenthal, P.B.1    Henderson, R.2
  • 57
    • 0019987933 scopus 로고
    • The correlation averaging of a regularly arranged bacterial cell envelope protein
    • Saxton WO, Baumeister W. 1982. The correlation averaging of a regularly arranged bacterial cell envelope protein. Journal of Microscopy 127:127-138. DOI:https://doi.org/10.1111/j.1365-2818.1982.tb00405.x
    • (1982) Journal of Microscopy , vol.127 , pp. 127-138
    • Saxton, W.O.1    Baumeister, W.2
  • 58
    • 84855818650 scopus 로고    scopus 로고
    • A Bayesian view on cryo-EM structure determination
    • Scheres SH. 2012. A Bayesian view on cryo-EM structure determination. Journal of Molecular Biology 415:406-418. DOI:https://doi.org/10.1016/j.jmb.2011.11.010
    • (2012) Journal of Molecular Biology , vol.415 , pp. 406-418
    • Scheres, S.H.1
  • 59
    • 0033380378 scopus 로고    scopus 로고
    • Scaling structure factor amplitudes in electron cryomicroscopy using X-Ray solution scattering
    • Schmid MF, Sherman MB, Matsudaira P, Tsuruta H, Chiu W. 1999. Scaling structure factor amplitudes in electron cryomicroscopy using X-Ray solution scattering. Journal of Structural Biology 128:51-57. DOI:https://doi.org/10.1006/jsbi.1999.4173
    • (1999) Journal of Structural Biology , vol.128 , pp. 51-57
    • Schmid, M.F.1    Sherman, M.B.2    Matsudaira, P.3    Tsuruta, H.4    Chiu, W.5
  • 60
    • 0030584127 scopus 로고    scopus 로고
    • Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments
    • Stehle T, Harrison SC. 1996. Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments. Structure 4:183-194. DOI:https://doi.org/10.1016/S0969-2126(96)00021-4
    • (1996) Structure , vol.4 , pp. 183-194
    • Stehle, T.1    Harrison, S.C.2
  • 61
    • 84953896483 scopus 로고    scopus 로고
    • CryoEM at IUCrJ: A new era
    • Subramaniam S, Kühlbrandt W, Henderson R. 2016. CryoEM at IUCrJ: a new era. IUCrJ 3:3-7. DOI:https://doi.org/10.1107/S2052252515023738
    • (2016) IUCrJ , vol.3 , pp. 3-7
    • Subramaniam, S.1    Kühlbrandt, W.2    Henderson, R.3
  • 62
    • 13444271681 scopus 로고    scopus 로고
    • Refined structure of the nicotinic acetylcholine receptor at 4A resolution
    • Unwin N. 2005. Refined structure of the nicotinic acetylcholine receptor at 4A resolution. Journal of Molecular Biology 346:967-989. DOI:https://doi.org/10.1016/j.jmb.2004.12.031
    • (2005) Journal of Molecular Biology , vol.346 , pp. 967-989
    • Unwin, N.1
  • 64
    • 0022325950 scopus 로고
    • Resolution of phase ambiguity in macromolecular crystallography
    • Wang BC. 1985. Resolution of phase ambiguity in macromolecular crystallography. Methods in Enzymology 115: 90-112. DOI:https://doi.org/10.1016/0076-6879(85)15009-3
    • (1985) Methods in Enzymology , vol.115 , pp. 90-112
    • Wang, B.C.1
  • 65
    • 84996565974 scopus 로고    scopus 로고
    • Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
    • Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. 2016. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5:e17219. DOI:https://doi.org/10.7554/eLife.17219
    • (2016) eLife , vol.5
    • Wang, R.Y.1    Song, Y.2    Barad, B.A.3    Cheng, Y.4    Fraser, J.S.5    DiMaio, F.6
  • 67
    • 84928019193 scopus 로고    scopus 로고
    • Elucidating factors important for monovalent cation selectivity in enzymes: E. Coli b-galactosidase as a model
    • Wheatley RW, Juers DH, Lev BB, Huber RE, Noskov SY. 2015. Elucidating factors important for monovalent cation selectivity in enzymes: E. coli b-galactosidase as a model. Physical Chemistry Chemical Physics 17: 10899-10909. DOI:https://doi.org/10.1039/C4CP04952G
    • (2015) Physical Chemistry Chemical Physics , vol.17 , pp. 10899-10909
    • Wheatley, R.W.1    Juers, D.H.2    Lev, B.B.3    Huber, R.E.4    Noskov, S.Y.5
  • 68
    • 0000984347 scopus 로고
    • Determination of absolute from relative X-ray intensity data
    • Wilson AJC. 1942. Determination of absolute from relative X-ray intensity data. Nature 150:152. DOI:https://doi.org/10.1038/150152a0
    • (1942) Nature , vol.150 , pp. 152
    • Wilson, A.J.C.1
  • 69
    • 0042238051 scopus 로고    scopus 로고
    • Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy
    • Yonekura K, Maki-Yonekura S, Namba K. 2003. Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424:643-650. DOI:https://doi.org/10.1038/nature01830
    • (2003) Nature , vol.424 , pp. 643-650
    • Yonekura, K.1    Maki-Yonekura, S.2    Namba, K.3
  • 70
    • 0030817618 scopus 로고    scopus 로고
    • Combining constraints for electron-density modification
    • Zhang KY, Cowtan K, Main P. 1997. Combining constraints for electron-density modification. Methods in Enzymology 277:53-64. DOI:https://doi.org/10.1016/s0076-6879(97)77006-x
    • (1997) Methods in Enzymology , vol.277 , pp. 53-64
    • Zhang, K.Y.1    Cowtan, K.2    Main, P.3
  • 71
    • 84929335211 scopus 로고    scopus 로고
    • Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase
    • Zhao J, Benlekbir S, Rubinstein JL. 2015. Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature 521:241-245. DOI:https://doi.org/10.1038/nature14365
    • (2015) Nature , vol.521 , pp. 241-245
    • Zhao, J.1    Benlekbir, S.2    Rubinstein, J.L.3


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