Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.
Journal
Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374
Informations de publication
Date de publication:
01 Jul 2024
01 Jul 2024
Historique:
received:
08
08
2023
accepted:
06
06
2024
medline:
2
7
2024
pubmed:
2
7
2024
entrez:
1
7
2024
Statut:
aheadofprint
Résumé
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAPs), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, here we use time-resolved cryogenic electron microscopy (cryo-EM) to capture four intermediates populated 120 ms or 500 ms after mixing Escherichia coli σ
Identifiants
pubmed: 38951624
doi: 10.1038/s41594-024-01349-9
pii: 10.1038/s41594-024-01349-9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Feklistov, A., Sharon, B. D., Darst, S. A. & Gross, C. A. Bacterial sigma factors: a historical, structural, and genomic perspective. Annu. Rev. Microbiol. 68, 357–376 (2014).
pubmed: 25002089
doi: 10.1146/annurev-micro-092412-155737
Gruber, T. M. & Gross, C. A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57, 441–466 (2003).
pubmed: 14527287
doi: 10.1146/annurev.micro.57.030502.090913
Zhang, G. et al. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98, 811–824 (1999).
pubmed: 10499798
doi: 10.1016/S0092-8674(00)81515-9
Shultzaberger, R. K., Chen, Z., Lewis, K. A. & Schneider, T. D. Anatomy of Escherichia coli σ
pubmed: 17189297
doi: 10.1093/nar/gkl956
Haugen, S. P. et al. rRNA promoter regulation by nonoptimal binding of σ region 1.2: an additional recognition element for RNA polymerase. Cell 125, 1069–1082 (2006).
pubmed: 16777598
doi: 10.1016/j.cell.2006.04.034
Ruff, E. F., Record, M. T. Jr & Artsimovitch, I. Initial events in bacterial transcription initiation. Biomolecules 5, 1035–1062 (2015).
pubmed: 26023916
pmcid: 4496709
doi: 10.3390/biom5021035
Saecker, R. M., Record, M. T. Jr & deHaseth, P. L. Mechanism of bacterial transcription initiation: RNA polymerase–promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J. Mol. Biol. 412, 754–771 (2011).
pubmed: 21371479
pmcid: 3440003
doi: 10.1016/j.jmb.2011.01.018
Saecker, R. M. et al. Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Proc. Natl Acad. Sci. USA 118, e2112877118 (2021).
pubmed: 34599106
pmcid: 8501879
doi: 10.1073/pnas.2112877118
Basu, R. S. et al. Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J. Biol. Chem. 289, 24549–24559 (2014).
pubmed: 24973216
pmcid: 4148879
doi: 10.1074/jbc.M114.584037
McClure, W. R. Rate-limiting steps in RNA chain initiation. Proc. Natl Acad. Sci. USA 77, 5634–5638 (1980).
pubmed: 6160577
pmcid: 350123
doi: 10.1073/pnas.77.10.5634
Chen, J. et al. Stepwise promoter melting by bacterial RNA polymerase. Mol. Cell 78, 275–288.e6 (2020).
pubmed: 32160514
pmcid: 7166197
doi: 10.1016/j.molcel.2020.02.017
Hubin, E. A. et al. Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. eLife 6, e22520 (2017).
pubmed: 28067618
pmcid: 5302886
doi: 10.7554/eLife.22520
Campbell, E. A. et al. Structure of the bacterial RNA polymerase promoter specificity σ subunit. Mol. Cell 9, 527–539 (2002).
pubmed: 11931761
doi: 10.1016/S1097-2765(02)00470-7
Feklistov, A. & Darst, S. A. Structural basis for promoter −10 element recognition by the bacterial RNA polymerase σ subunit. Cell 147, 1257–1269 (2011).
pubmed: 22136875
pmcid: 3245737
doi: 10.1016/j.cell.2011.10.041
Bae, B., Feklistov, A., Lass-Napiorkowska, A., Landick, R. & Darst, S. A. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife 4, e08504 (2015).
pubmed: 26349032
pmcid: 4593229
doi: 10.7554/eLife.08504
Mekler, V. et al. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase–promoter open complex. Cell 108, 599–614 (2002).
pubmed: 11893332
doi: 10.1016/S0092-8674(02)00667-0
Bae, B. et al. Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ
pubmed: 24218560
pmcid: 3856789
doi: 10.1073/pnas.1314576110
Hubin, E. A., Lilic, M., Darst, S. A. & Campbell, E. A. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. Nat. Commun. 8, 16072 (2017).
pubmed: 28703128
pmcid: 5511352
doi: 10.1038/ncomms16072
Chen, J., Boyaci, H. & Campbell, E. A. Diverse and unified mechanisms of transcription initiation in bacteria. Nat. Rev. Microbiol. 19, 95–109 (2021).
pubmed: 33122819
doi: 10.1038/s41579-020-00450-2
Boyaci, H., Chen, J., Jansen, R., Darst, S. A. & Campbell, E. A. Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding. Nature 565, 382–385 (2019).
pubmed: 30626968
pmcid: 6399747
doi: 10.1038/s41586-018-0840-5
Dandey, V. P. et al. Time-resolved cryo-EM using Spotiton. Nat. Methods 17, 897–900 (2020).
pubmed: 32778833
pmcid: 7799389
doi: 10.1038/s41592-020-0925-6
Punjani, A. & Fleet, D. J. 3D variability analysis: resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J. Struct. Biol. 213, 107702 (2021).
pubmed: 33582281
doi: 10.1016/j.jsb.2021.107702
Wei, H. et al. Optimizing ‘self-wicking’ nanowire grids. J. Struct. Biol. 202, 170–174 (2018).
pubmed: 29317278
pmcid: 5864531
doi: 10.1016/j.jsb.2018.01.001
Wu, J. L. Y., Tellkamp, F., Khajehpour, M., Robertson, W. D. & Miller, R. J. D. Rapid mixing of colliding picoliter liquid droplets delivered through-space from piezoelectric-actuated pipettes characterized by time-resolved fluorescence monitoring. Rev. Sci. Instrum. 90, 055109 (2019).
pubmed: 31153275
doi: 10.1063/1.5050270
Chen, J., Noble, A. J., Kang, J. Y. & Darst, S. A. Eliminating effects of particle adsorption to the air/water interface in single-particle cryo-electron microscopy: bacterial RNA polymerase and CHAPSO. J. Struct. Biol. X 1, 100005 (2019).
pubmed: 32285040
pmcid: 7153306
Tsodikov, O. V. & Record, M. T. Jr General method of analysis of kinetic equations for multistep reversible mechanisms in the single-exponential regime: application to kinetics of open complex formation between Eσ
pubmed: 10049315
pmcid: 1300111
doi: 10.1016/S0006-3495(99)77294-2
Saecker, R. M. et al. Kinetic studies and structural models of the association of E. coli σ
pubmed: 12054861
doi: 10.1016/S0022-2836(02)00293-0
Gnatt, A. L., Cramer, P., Fu, J., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution. Science 292, 1876–1882 (2001).
pubmed: 11313499
doi: 10.1126/science.1059495
Landick, R. RNA polymerase clamps down. Cell 105, 567–570 (2001).
pubmed: 11389826
doi: 10.1016/S0092-8674(01)00381-6
Darst, S. A. et al. Conformational flexibility of bacterial RNA polymerase. Proc. Natl Acad. Sci. USA 99, 4296–4301 (2002).
pubmed: 11904365
pmcid: 123642
doi: 10.1073/pnas.052054099
Weixlbaumer, A., Leon, K., Landick, R. & Darst, S. A. Structural basis of transcriptional pausing in bacteria. Cell 152, 431–441 (2013).
pubmed: 23374340
pmcid: 3564060
doi: 10.1016/j.cell.2012.12.020
Chakraborty, A. et al. Opening and closing of the bacterial RNA polymerase clamp. Science 337, 591–595 (2012).
pubmed: 22859489
pmcid: 3626110
doi: 10.1126/science.1218716
Chen, J. et al. E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation. eLife 8, e49375 (2019).
pubmed: 31841111
pmcid: 6970531
doi: 10.7554/eLife.49375
Unarta, I. C. et al. Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov state model. Proc. Natl Acad. Sci. USA 118, e2024324118 (2021).
pubmed: 33883282
pmcid: 8092612
doi: 10.1073/pnas.2024324118
Dey, S. et al. Structural insights into RNA-mediated transcription regulation in bacteria. Mol. Cell 82, 3885–3900.e10 (2022).
pubmed: 36220101
doi: 10.1016/j.molcel.2022.09.020
Mukhopadhyay, J. et al. The RNA polymerase ‘switch region’ is a target for inhibitors. Cell 135, 295–307 (2008).
pubmed: 18957204
pmcid: 2580802
doi: 10.1016/j.cell.2008.09.033
Belogurov, G. A. et al. Transcription inactivation through local refolding of the RNA polymerase structure. Nature 457, 332–335 (2008).
pubmed: 18946472
pmcid: 2628454
doi: 10.1038/nature07510
Srivastava, A. et al. New target for inhibition of bacterial RNA polymerase: a ’switch region
pubmed: 21862392
pmcid: 3196380
doi: 10.1016/j.mib.2011.07.030
Lin, W. et al. Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3). Mol. Cell 70, 60–71.e15 (2018).
pubmed: 29606590
pmcid: 6205224
doi: 10.1016/j.molcel.2018.02.026
Boyaci, H. et al. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. eLife 7, e34823 (2018).
pubmed: 29480804
pmcid: 5837556
doi: 10.7554/eLife.34823
Cao, X. et al. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature 604, 541–545 (2022).
pubmed: 35388215
pmcid: 9635844
doi: 10.1038/s41586-022-04545-z
Endres, D. M. & Schindelin, J. E. A new metric for probability distributions. IEEE Trans. Inf. Theory 49, 1858 (2003).
doi: 10.1109/TIT.2003.813506
Sreenivasan, R. et al. Fluorescence-detected conformational changes in duplex DNA in open complex formation by Escherichia coli RNA polymerase: upstream wrapping and downstream bending precede clamp opening and insertion of the downstream duplex. Biochemistry 59, 1565–1581 (2020).
pubmed: 32216369
doi: 10.1021/acs.biochem.0c00098
Davis, C. A., Bingman, C. A., Landick, R., Record, M. T. Jr & Saecker, R. M. Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA 104, 7833–7838 (2007).
pubmed: 17470797
pmcid: 1876533
doi: 10.1073/pnas.0609888104
Craig, M. L. et al. DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase–promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol. 283, 741–756 (1998).
pubmed: 9790837
doi: 10.1006/jmbi.1998.2129
Roy, S., Lim, H. M., Liu, M. & Adhya, S. Asynchronous basepair openings in transcription initiation: CRP enhances the rate-limiting step. EMBO J. 23, 869–875 (2004).
pubmed: 14963488
pmcid: 381006
doi: 10.1038/sj.emboj.7600098
Heyduk, E. & Heyduk, T. Next generation sequencing-based parallel analysis of melting kinetics of 4096 variants of a bacterial promoter. Biochemistry 53, 282–292 (2014).
pubmed: 24359527
doi: 10.1021/bi401277w
Callaci, S., Heyduk, E. & Heyduk, T. Conformational changes of Escherichia coli RNA polymerase σ
pubmed: 9830052
doi: 10.1074/jbc.273.49.32995
Lilic, M., Darst, S. A. & Campbell, E. A. Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7. Mol. Cell 81, 2875–2886.e5 (2021).
pubmed: 34171296
pmcid: 8311663
doi: 10.1016/j.molcel.2021.05.017
Feklistov, A. et al. RNA polymerase motions during promoter melting. Science 356, 863–866 (2017).
pubmed: 28546214
pmcid: 5696265
doi: 10.1126/science.aam7858
He, Y., Fang, J., Taatjes, D. J. & Nogales, E. Structural visualization of key steps in human transcription initiation. Nature 495, 481–486 (2013).
pubmed: 23446344
pmcid: 3612373
doi: 10.1038/nature11991
Schulz, S. et al. TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. Proc. Natl Acad. Sci. USA 113, E1816–E1825 (2016).
pubmed: 26979960
pmcid: 4822635
doi: 10.1073/pnas.1515817113
Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8 Ångstrom resolution. Science 292, 1863–1876 (2001).
pubmed: 11313498
doi: 10.1126/science.1059493
Lane, W. J. & Darst, S. A. Molecular evolution of multisubunit RNA polymerases: structural analysis. J. Mol. Biol. 395, 686–704 (2010).
pubmed: 19895816
doi: 10.1016/j.jmb.2009.10.063
Travers, A. A. Promoter sequence for stringent control of bacterial ribonucleic acid synthesis. J. Bacteriol. 141, 973–976 (1980).
pubmed: 6154042
pmcid: 293725
doi: 10.1128/jb.141.2.973-976.1980
Haugen, S. P., Ross, W., Manrique, M. & Gourse, R. L. Fine structure of the promoter–σ region 1.2 interaction. Proc. Natl Acad. Sci. USA 105, 3292–3297 (2008).
pubmed: 18287032
pmcid: 2265156
doi: 10.1073/pnas.0709513105
Vvedenskaya, I. O. et al. Massively Systematic Transcript End Readout, ‘MASTER’: transcription start site selection, transcriptional slippage, and transcript yields. Mol. Cell 60, 953–965 (2015).
pubmed: 26626484
pmcid: 4688149
doi: 10.1016/j.molcel.2015.10.029
Winkelman, J. T. et al. Multiplexed protein–DNA cross-linking: scrunching in transcription start site selection. Science 351, 1090–1093 (2016).
pubmed: 26941320
pmcid: 4797950
doi: 10.1126/science.aad6881
Gourse, R. L. et al. Transcriptional responses to ppGpp and DksA. Annu. Rev. Microbiol. 72, 163–184 (2018).
pubmed: 30200857
pmcid: 6586590
doi: 10.1146/annurev-micro-090817-062444
Roche, J. & Royer, C. A. Lessons from pressure denaturation of proteins. J. R. Soc. Interface 15, 20180244 (2018).
pubmed: 30282759
pmcid: 6228469
doi: 10.1098/rsif.2018.0244
Guvench, O. & Brooks, C. L. Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed β-hairpin ‘trpzip2’. J. Am. Chem. Soc. 127, 4668–4674 (2005).
pubmed: 15796532
doi: 10.1021/ja043492e
Kovacic, R. T. The 0°C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5. J. Biol. Chem. 262, 13654–13661 (1987).
pubmed: 3308880
doi: 10.1016/S0021-9258(19)76477-1
Cowing, D. W., Mecsas, J., Record, M. T. & Gross, C. A. Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor σ
pubmed: 2693737
doi: 10.1016/0022-2836(89)90128-9
Schickor, P., Metzger, W., Werel, W., Lederer, H. & Heumann, H. Topography of intermediates in transcription initiation of E. coli. EMBO J. 9, 2215–2220 (1990).
pubmed: 2192861
pmcid: 551945
doi: 10.1002/j.1460-2075.1990.tb07391.x
Rutherford, S. T., Villers, C. L., Lee, J.-H., Ross, W. & Gourse, R. L. Allosteric control of Escherichia coli rRNA promoter complexes by DksA. Genes Dev. 23, 236–248 (2009).
pubmed: 19171784
pmcid: 2648540
doi: 10.1101/gad.1745409
Sasse-Dwight, S. & Gralla, J. D. KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem. 264, 8074–8081 (1989).
pubmed: 2722774
doi: 10.1016/S0021-9258(18)83152-0
Galas, D. J. & Schmitz, A. DNAse footprinting: a simple method for the detection of protein–DNA binding specificity. Nucleic Acids Res. 5, 3157–3170 (1978).
pubmed: 212715
pmcid: 342238
doi: 10.1093/nar/5.9.3157
Tullius, T. D. DNA footprinting with hydroxyl radical. Nature 332, 663–664 (1988).
pubmed: 2833707
doi: 10.1038/332663a0
Gries, T. J., Kontur, W. S., Capp, M. W., Saecker, R. M. & Record, M. T. Jr One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex. Proc. Natl Acad. Sci. USA 107, 10418–10423 (2010).
pubmed: 20483995
pmcid: 2890804
doi: 10.1073/pnas.1000967107
Altan-Bonnet, G., Libchaber, A. & Krichevsky, O. Bubble dynamics in double-stranded DNA. Phys. Rev. Lett. 90, 138101 (2003).
pubmed: 12689326
doi: 10.1103/PhysRevLett.90.138101
Nicy, Chakraborty, D. & Wales, D. J. Energy landscapes for base-flipping in a model DNA duplex. J. Phys. Chem. B 126, 3012–3028 (2022).
pubmed: 35427136
pmcid: 9098180
doi: 10.1021/acs.jpcb.2c00340
Łoziński, T. & Wierzchowski, K. L. Inactivation and destruction by KMnO
pubmed: 12927830
doi: 10.1016/S0003-2697(03)00381-6
Rogozina, A., Zaychikov, E., Buckle, M., Heumann, H. & Sclavi, B. DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37°C and results in the accumulation of an off-pathway intermediate. Nucleic Acids Res. 37, 5390–5404 (2009).
pubmed: 19578065
pmcid: 2760793
doi: 10.1093/nar/gkp560
Schroeder, L. A. et al. Evidence for a tyrosine–adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA. J. Mol. Biol. 385, 339–349 (2009).
pubmed: 18976666
doi: 10.1016/j.jmb.2008.10.023
Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ 6, 5–17 (2018).
doi: 10.1107/S205225251801463X
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).
pubmed: 17681537
doi: 10.1016/j.jmb.2007.05.022
Cardone, G., Heymann, J. B. & Steven, A. C. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 184, 226–236 (2013).
pubmed: 23954653
doi: 10.1016/j.jsb.2013.08.002
Davis, C. A., Capp, M. W., Record, M. T. Jr & Saecker, R. M. The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA 102, 285–290 (2005).
pubmed: 15626761
doi: 10.1073/pnas.0405779102
Budell, W. C., Allegri, L., Dandey, V., Potter, C. S. & Carragher, B. Cryo-electron microscopic grid preparation for time-resolved studies using a novel robotic system, Spotiton. J. Vis. Exp. https://doi.org/10.3791/62271 (2021).
doi: 10.3791/62271
pubmed: 33720116
Razinkov, I. et al. A new method for vitrifying samples for cryoEM. J. Struct. Biol. 195, 190–198 (2016).
pubmed: 27288865
pmcid: 5464370
doi: 10.1016/j.jsb.2016.06.001
Morin, A. et al. Collaboration gets the most out of software. eLife 2, e01456 (2013).
pubmed: 24040512
pmcid: 3771563
doi: 10.7554/eLife.01456
Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005).
pubmed: 15890530
doi: 10.1016/j.jsb.2005.03.010
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
pubmed: 28250466
pmcid: 5494038
doi: 10.1038/nmeth.4193
Scheres, S. H. W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
pubmed: 23000701
pmcid: 3690530
doi: 10.1016/j.jsb.2012.09.006
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473
doi: 10.1038/nmeth.4169
Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).
pubmed: 33257830
doi: 10.1038/s41592-020-00990-8
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
pubmed: 30412051
pmcid: 6250425
doi: 10.7554/eLife.42166
Bai, X., Rajendra, E., Yang, G., Shi, Y. & Scheres, S. H. W. Sampling the conformational space of the catalytic subunit of human γ-secretase. eLife 4, e11182 (2015).
pubmed: 26623517
pmcid: 4718806
doi: 10.7554/eLife.11182
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
pubmed: 15264254
doi: 10.1002/jcc.20084
Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
pubmed: 28671674
pmcid: 5533649
doi: 10.1038/nmeth.4347
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
pubmed: 20124702
pmcid: 2815670
doi: 10.1107/S0907444909052925
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
pubmed: 20383002
pmcid: 2852313
doi: 10.1107/S0907444910007493
Kang, J. Y. et al. An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options. Proc. Natl Acad. Sci. USA 120, e2215945120 (2023).
pubmed: 36795753
pmcid: 9974457
doi: 10.1073/pnas.2215945120
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).
pubmed: 20057044
doi: 10.1107/S0907444909042073
Henderson, R. et al. Outcome of the first electron microscopy validation task force meeting. Structure 20, 205–214 (2012).
pubmed: 22325770
doi: 10.1016/j.str.2011.12.014