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Volumn 541, Issue 7636, 2017, Pages 242-246

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

(38)  Stagno, J R a   Liu, Y a   Bhandari, Y R a   Conrad, C E b   Panja, S c   Swain, M a   Fan, L a   Nelson, G b   Li, C b   Wendel, D R a   White, T A d   Coe, J D b   Wiedorn, M O d,e   Knoska, J d,e   Oberthuer, D d   Tuckey, R A a   Yu, P a   Dyba, M a   Tarasov, S G a   Weierstall, U b   more..

d DESY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; APTAMER; NANOCRYSTAL; RNA; 5' UNTRANSLATED REGION; BACTERIAL RNA; LIGAND; RIBOSWITCH;

EID: 85016142050     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature20599     Document Type: Article
Times cited : (230)

References (56)
  • 1
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C., Breaker, R. R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113, 577-586 (2003).
    • (2003) Cell , vol.113 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 2
    • 0036753365 scopus 로고    scopus 로고
    • Genetic control by a metabolite binding mRNA
    • Nahvi, A., et al. Genetic control by a metabolite binding mRNA. Chem. Biol. 9, 1043 (2002).
    • (2002) Chem. Biol. , vol.9 , pp. 1043
    • Nahvi, A.1
  • 4
    • 0033762447 scopus 로고    scopus 로고
    • Analyzing protein functions in four dimensions
    • Hajdu, J., et al. Analyzing protein functions in four dimensions. Nat. Struct. Biol. 7, 1006-1012 (2000).
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 1006-1012
    • Hajdu, J.1
  • 5
    • 84864004802 scopus 로고    scopus 로고
    • High-resolution protein structure determination by serial femtosecond crystallography
    • Boutet, S., et al. High-resolution protein structure determination by serial femtosecond crystallography. Science 337, 362-364 (2012).
    • (2012) Science , vol.337 , pp. 362-364
    • Boutet, S.1
  • 6
    • 79551658540 scopus 로고    scopus 로고
    • Femtosecond X-ray protein nanocrystallography
    • Chapman, H. N., et al. Femtosecond X-ray protein nanocrystallography. Nature 470, 73-77 (2011).
    • (2011) Nature , vol.470 , pp. 73-77
    • Chapman, H.N.1
  • 7
    • 10644250950 scopus 로고    scopus 로고
    • Structural basis for discriminative regulation of gene expression by adenine-and guanine-sensing mRNAs
    • Serganov, A., et al. Structural basis for discriminative regulation of gene expression by adenine-and guanine-sensing mRNAs. Chem. Biol. 11, 1729-1741 (2004).
    • (2004) Chem. Biol. , vol.11 , pp. 1729-1741
    • Serganov, A.1
  • 8
    • 0142075327 scopus 로고    scopus 로고
    • Genetic control by metabolite-binding riboswitches
    • Winkler, W. C., Breaker, R. R. Genetic control by metabolite-binding riboswitches. ChemBioChem 4, 1024-1032 (2003).
    • (2003) ChemBioChem , vol.4 , pp. 1024-1032
    • Winkler, W.C.1    Breaker, R.R.2
  • 9
    • 84865231710 scopus 로고    scopus 로고
    • Structure and mechanism of purine-binding riboswitches
    • Batey, R. T. Structure and mechanism of purine-binding riboswitches. Q. Rev. Biophys. 45, 345-381 (2012).
    • (2012) Q. Rev. Biophys. , vol.45 , pp. 345-381
    • Batey, R.T.1
  • 10
    • 84885985615 scopus 로고    scopus 로고
    • Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
    • Di Palma, F., Colizzi, F., Bussi, G. Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch. RNA 19, 1517-1524 (2013).
    • (2013) RNA , vol.19 , pp. 1517-1524
    • Di Palma, F.1    Colizzi, F.2    Bussi, G.3
  • 11
    • 33845942987 scopus 로고    scopus 로고
    • The adenine riboswitch. A new gene regulation mechanism.
    • Lemay, J. F., Lafontaine, D. A. [The adenine riboswitch: a new gene regulation mechanism]. Med. Sci. (Paris) 22, 1053-1059 (2006).
    • (2006) Med. Sci. (Paris) , vol.22 , pp. 1053-1059
    • Lemay, J.F.1    Lafontaine, D.A.2
  • 12
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanineresponsive riboswitch complexed with the metabolite hypoxanthine
    • Batey, R. T., Gilbert, S. D., Montange, R. K. Structure of a natural guanineresponsive riboswitch complexed with the metabolite hypoxanthine. Nature 432, 411-415 (2004).
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 13
    • 84929317576 scopus 로고    scopus 로고
    • Dramatic improvement of crystals of large RNAs by cation replacement and dehydration
    • Zhang, J., Ferré-D'Amaré, A. R. Dramatic improvement of crystals of large RNAs by cation replacement and dehydration. Structure 22, 1363-1371 (2014).
    • (2014) Structure , vol.22 , pp. 1363-1371
    • Zhang, J.1    Ferré-D'Amaré, A.R.2
  • 14
    • 34447548824 scopus 로고    scopus 로고
    • Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control
    • Rieder, R., Lang, K., Graber, D., Micura, R. Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control. ChemBioChem 8, 896-902 (2007).
    • (2007) ChemBioChem , vol.8 , pp. 896-902
    • Rieder, R.1    Lang, K.2    Graber, D.3    Micura, R.4
  • 15
    • 33646768226 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain
    • Gilbert, S. D., Stoddard, C. D., Wise, S. J., Batey, R. T. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J. Mol. Biol. 359, 754-768 (2006).
    • (2006) J. Mol. Biol. , vol.359 , pp. 754-768
    • Gilbert, S.D.1    Stoddard, C.D.2    Wise, S.J.3    Batey, R.T.4
  • 16
    • 77951236405 scopus 로고    scopus 로고
    • Riboswitch structure: An internal residue mimicking the purine ligand
    • Delfosse, V., et al. Riboswitch structure: an internal residue mimicking the purine ligand. Nucleic Acids Res. 38, 2057-2068 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2057-2068
    • Delfosse, V.1
  • 17
    • 79960114180 scopus 로고    scopus 로고
    • Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation
    • Jenkins, J. L., Krucinska, J., McCarty, R. M., Bandarian, V., Wedekind, J. E. Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. J. Biol. Chem. 286, 24626-24637 (2011).
    • (2011) J. Biol. Chem. , vol.286 , pp. 24626-24637
    • Jenkins, J.L.1    Krucinska, J.2    McCarty, R.M.3    Bandarian, V.4    Wedekind, J.E.5
  • 18
    • 84966311116 scopus 로고    scopus 로고
    • Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein
    • Pande, K., et al. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science 352, 725-729 (2016).
    • (2016) Science , vol.352 , pp. 725-729
    • Pande, K.1
  • 19
    • 84918582756 scopus 로고    scopus 로고
    • Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein
    • Tenboer, J., et al. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science 346, 1242-1246 (2014).
    • (2014) Science , vol.346 , pp. 1242-1246
    • Tenboer, J.1
  • 20
    • 84944769107 scopus 로고    scopus 로고
    • Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation
    • Barends, T. R., et al. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 350, 445-450 (2015).
    • (2015) Science , vol.350 , pp. 445-450
    • Barends, T.R.1
  • 21
    • 0023650022 scopus 로고
    • Millisecond X-ray diffraction and the first electron density map from Laue photographs of a protein crystal
    • Hajdu, J., et al. Millisecond X-ray diffraction and the first electron density map from Laue photographs of a protein crystal. Nature 329, 178-181 (1987).
    • (1987) Nature , vol.329 , pp. 178-181
    • Hajdu, J.1
  • 22
    • 84939785300 scopus 로고    scopus 로고
    • Double-focusing mixing jet for XFEL study of chemical kinetics
    • Wang, D., Weierstall, U., Pollack, L., Spence, J. Double-focusing mixing jet for XFEL study of chemical kinetics. J. Synchrotron Radiat. 21, 1364-1366 (2014).
    • (2014) J. Synchrotron Radiat. , vol.21 , pp. 1364-1366
    • Wang, D.1    Weierstall, U.2    Pollack, L.3    Spence, J.4
  • 23
    • 84878734295 scopus 로고    scopus 로고
    • Mix and inject: Reaction initiation by diffusion for time-resolved acromolecular crystallography
    • Schmidt, M. Mix and inject: reaction initiation by diffusion for time-resolved acromolecular crystallography. Adv. Condens. Matter Phys. 2013, 167276 (2013).
    • (2013) Adv. Condens. Matter Phys. , vol.2013 , pp. 167276
    • Schmidt, M.1
  • 24
    • 4744343045 scopus 로고    scopus 로고
    • Linkage between dynamics and catalysis in a thermophilicmesophilic enzyme pair
    • Wolf-Watz, M., et al. Linkage between dynamics and catalysis in a thermophilicmesophilic enzyme pair. Nat. Struct. Mol. Biol. 11, 945-949 (2004).
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 945-949
    • Wolf-Watz, M.1
  • 26
    • 0024991348 scopus 로고
    • Calcium binding sites in tomato bushy stunt virus visualized by Laue crystallography
    • Campbell, J. W., et al. Calcium binding sites in tomato bushy stunt virus visualized by Laue crystallography. J. Mol. Biol. 214, 627-632 (1990).
    • (1990) J. Mol. Biol. , vol.214 , pp. 627-632
    • Campbell, J.W.1
  • 27
    • 84908221627 scopus 로고    scopus 로고
    • Modelling dynamics in protein crystal structures by ensemble refinement
    • Burnley, B. T., Afonine, P. V., Adams, P. D., Gros, P. Modelling dynamics in protein crystal structures by ensemble refinement. eLife 1, e00311 (2012).
    • (2012) ELife , vol.1 , pp. e00311
    • Burnley, B.T.1    Afonine, P.V.2    Adams, P.D.3    Gros, P.4
  • 28
    • 80052602449 scopus 로고    scopus 로고
    • Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch
    • Huang, L., Ishibe-Murakami, S., Patel, D. J., Serganov, A. Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch. Proc. Natl Acad. Sci. USA 108, 14801-14806 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 14801-14806
    • Huang, L.1    Ishibe-Murakami, S.2    Patel, D.J.3    Serganov, A.4
  • 29
    • 84875043544 scopus 로고    scopus 로고
    • Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution
    • Haller, A., Altman, R. B., Soulière, M. F., Blanchard, S. C., Micura, R. Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution. Proc. Natl Acad. Sci. USA 110, 4188-4193 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 4188-4193
    • Haller, A.1    Altman, R.B.2    Soulière, M.F.3    Blanchard, S.C.4    Micura, R.5
  • 30
    • 84978438758 scopus 로고    scopus 로고
    • Imaging enzyme kinetics at atomic resolution
    • Spence, J., Lattman, E. Imaging enzyme kinetics at atomic resolution. IUCrJ 3, 228-229 (2016).
    • (2016) IUCrJ , vol.3 , pp. 228-229
    • Spence, J.1    Lattman, E.2
  • 31
    • 84934326542 scopus 로고    scopus 로고
    • Synthesis and applications of RNAs with position-selective labelling and mosaic composition
    • Liu, Y., et al. Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature 522, 368-372 (2015).
    • (2015) Nature , vol.522 , pp. 368-372
    • Liu, Y.1
  • 32
    • 84939784819 scopus 로고    scopus 로고
    • A novel inert crystal delivery medium for serial femtosecond crystallography
    • Conrad, C. E., et al. A novel inert crystal delivery medium for serial femtosecond crystallography. IUCrJ 2, 421-430 (2015).
    • (2015) IUCrJ , vol.2 , pp. 421-430
    • Conrad, C.E.1
  • 33
    • 0032422462 scopus 로고    scopus 로고
    • A simple mechanical mixer for small viscous lipid-containing samples
    • Cheng, A., Hummel, B., Qiu, H., Caffrey, M. A simple mechanical mixer for small viscous lipid-containing samples. Chem. Phys. Lipids 95, 11-21 (1998).
    • (1998) Chem. Phys. Lipids , vol.95 , pp. 11-21
    • Cheng, A.1    Hummel, B.2    Qiu, H.3    Caffrey, M.4
  • 34
    • 84894037590 scopus 로고    scopus 로고
    • Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography
    • Weierstall, U., et al. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat. Commun. 5, 3309 (2014).
    • (2014) Nat. Commun. , vol.5 , pp. 3309
    • Weierstall, U.1
  • 35
    • 84901819736 scopus 로고    scopus 로고
    • Cheetah: Software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
    • Barty, A., et al. Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data. J. Appl. Crystallogr. 47, 1118-1131 (2014).
    • (2014) J. Appl. Crystallogr. , vol.47 , pp. 1118-1131
    • Barty, A.1
  • 36
    • 84859777150 scopus 로고    scopus 로고
    • CrystFEL: A software suite for snapshot serial crystallography
    • White, T. A., et al. CrystFEL: a software suite for snapshot serial crystallography. J. Appl. Crystallogr. 45, 335-341 (2012).
    • (2012) J. Appl. Crystallogr. , vol.45 , pp. 335-341
    • White, T.A.1
  • 37
    • 79951928807 scopus 로고    scopus 로고
    • Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals
    • Kirian, R. A., et al. Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. Acta Crystallogr. A 67, 131-140 (2011).
    • (2011) Acta Crystallogr. A , vol.67 , pp. 131-140
    • Kirian, R.A.1
  • 38
    • 84879345494 scopus 로고    scopus 로고
    • Crystallographic data processing for free-electron laser sources
    • White, T. A., et al. Crystallographic data processing for free-electron laser sources. Acta Crystallogr. D 69, 1231-1240 (2013).
    • (2013) Acta Crystallogr. D , vol.69 , pp. 1231-1240
    • White, T.A.1
  • 39
    • 84861425552 scopus 로고    scopus 로고
    • Linking crystallographic model and data quality
    • Karplus, P. A., Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030-1033 (2012).
    • (2012) Science , vol.336 , pp. 1030-1033
    • Karplus, P.A.1    Diederichs, K.2
  • 40
    • 0000952473 scopus 로고
    • On the treatment of negative intensity observations
    • French, G. S., Wilson, K. S. On the treatment of negative intensity observations. Acta Crystallogr. A 34, 517-525 (1978).
    • (1978) Acta Crystallogr. A , vol.34 , pp. 517-525
    • French, G.S.1    Wilson, K.S.2
  • 41
    • 34447508216 scopus 로고    scopus 로고
    • Phaser crystallographic software
    • McCoy, A. J., et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
    • (2007) J. Appl. Crystallogr. , vol.40 , pp. 658-674
    • McCoy, A.J.1
  • 42
    • 14244272868 scopus 로고    scopus 로고
    • PHENIX: Building new software for automated crystallographic structure determination
    • Adams, P. D., et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948-1954 (2002).
    • (2002) Acta Crystallogr. D , vol.58 , pp. 1948-1954
    • Adams, P.D.1
  • 43
    • 79953763877 scopus 로고    scopus 로고
    • REFMAC5 for the refinement of macromolecular crystal structures
    • Murshudov, G. N., et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355-367 (2011).
    • (2011) Acta Crystallogr. D , vol.67 , pp. 355-367
    • Murshudov, G.N.1
  • 44
    • 84871957573 scopus 로고    scopus 로고
    • Correcting pervasive errors in RNA crystallography through enumerative structure prediction
    • Chou, F. C., Sripakdeevong, P., Dibrov, S. M., Hermann, T., Das, R. Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nat. Methods 10, 74-76 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 74-76
    • Chou, F.C.1    Sripakdeevong, P.2    Dibrov, S.M.3    Hermann, T.4    Das, R.5
  • 45
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley, P., Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
    • (2004) Acta Crystallogr. D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 47
    • 70349783815 scopus 로고    scopus 로고
    • A method for helical RNA global structure determination in solution using small-angle X-ray scattering and NMR measurements
    • Wang, J., et al. A method for helical RNA global structure determination in solution using small-angle X-ray scattering and NMR measurements. J. Mol. Biol. 393, 717-734 (2009).
    • (2009) J. Mol. Biol. , vol.393 , pp. 717-734
    • Wang, J.1
  • 48
    • 84861049339 scopus 로고    scopus 로고
    • Reliable structural interpretation of small-angle scattering data from bio-molecules in solution-the importance of quality control and a standard reporting framework
    • Jacques, D. A., Guss, J. M., Trewhella, J. Reliable structural interpretation of small-angle scattering data from bio-molecules in solution-the importance of quality control and a standard reporting framework. BMC Struct. Biol. 12, 9 (2012).
    • (2012) BMC Struct. Biol. , vol.12 , pp. 9
    • Jacques, D.A.1    Guss, J.M.2    Trewhella, J.3
  • 49
    • 33644861376 scopus 로고    scopus 로고
    • X-ray diffraction fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation
    • Zuo, X., et al. X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proc. Natl Acad. Sci. USA 103, 3534-3539 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 3534-3539
    • Zuo, X.1
  • 50
    • 76149130049 scopus 로고    scopus 로고
    • X-ray scattering combined with coordinatebased analyses for applications in natural and artificial photosynthesis
    • Tiede, D. M., Mardis, K. L., Zuo, X. X-ray scattering combined with coordinatebased analyses for applications in natural and artificial photosynthesis. Photosynth. Res. 102, 267-279 (2009).
    • (2009) Photosynth. Res. , vol.102 , pp. 267-279
    • Tiede, D.M.1    Mardis, K.L.2    Zuo, X.3
  • 51
    • 41449107849 scopus 로고    scopus 로고
    • Global molecular structure and interfaces: Refining an RNA:RNA complex structure using solution X-ray scattering data
    • Zuo, X., et al. Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. J. Am. Chem. Soc. 130, 3292-3293 (2008).
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 3292-3293
    • Zuo, X.1
  • 52
    • 0035880916 scopus 로고    scopus 로고
    • Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces
    • Nadassy, K., Tomás-Oliveira, I., Alberts, I., Janin, J., Wodak, S. J. Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces. Nucleic Acids Res. 29, 3362-3376 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 3362-3376
    • Nadassy, K.1    Tomás-Oliveira, I.2    Alberts, I.3    Janin, J.4    Wodak, S.J.5
  • 53
    • 12544256134 scopus 로고    scopus 로고
    • Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly
    • Voss, N. R., Gerstein, M. Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly. J. Mol. Biol. 346, 477-492 (2005).
    • (2005) J. Mol. Biol. , vol.346 , pp. 477-492
    • Voss, N.R.1    Gerstein, M.2
  • 55
    • 84886772732 scopus 로고    scopus 로고
    • An unusual topological structure of the HIV-1 Rev response element
    • Fang, X., et al. An unusual topological structure of the HIV-1 Rev response element. Cell 155, 594-605 (2013).
    • (2013) Cell , vol.155 , pp. 594-605
    • Fang, X.1
  • 56
    • 84887098014 scopus 로고    scopus 로고
    • Structure and dynamics of full-length HIV-1 capsid protein in solution
    • Deshmukh, L., et al. Structure and dynamics of full-length HIV-1 capsid protein in solution. J. Am. Chem. Soc. 135, 16133-16147 (2013).
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 16133-16147
    • Deshmukh, L.1


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