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James M. Holton, Ph.D. - Publications

Affiliations: 
2001 University of California, Berkeley, Berkeley, CA, United States 
Area:
host-pathogen interactions, motions in proteins
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63 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, et al. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nature Chemistry. PMID 37723259 DOI: 10.1038/s41557-023-01329-4  0.515
2023 Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N. Large language models generate functional protein sequences across diverse families. Nature Biotechnology. PMID 36702895 DOI: 10.1038/s41587-022-01618-2  0.456
2022 Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Science Advances. 8: eabo5083. PMID 35622909 DOI: 10.1126/sciadv.abo5083  0.539
2022 Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. Biorxiv : the Preprint Server For Biology. PMID 35169801 DOI: 10.1101/2022.02.07.479477  0.535
2021 Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, ... ... Holton JM, et al. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Science Advances. 7. PMID 33853786 DOI: 10.1126/sciadv.abf8711  0.518
2020 Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, ... ... Holton JM, et al. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. Biorxiv : the Preprint Server For Biology. PMID 33269349 DOI: 10.1101/2020.11.24.393405  0.519
2020 de la Mora E, Coquelle N, Bury CS, Rosenthal M, Holton JM, Carmichael I, Garman EF, Burghammer M, Colletier JP, Weik M. Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures. Proceedings of the National Academy of Sciences of the United States of America. PMID 32047034 DOI: 10.1073/Pnas.1821522117  0.342
2019 Bruning JM, Wang Y, Oltrabella F, Tian B, Kholodar SA, Liu H, Bhattacharya P, Guo S, Holton JM, Fletterick RJ, Jacobson MP, England PM. Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite. Cell Chemical Biology. PMID 30853418 DOI: 10.1016/J.Chembiol.2019.02.002  0.306
2019 Holton JM. Challenge data set for macromolecular multi-microcrystallography. Acta Crystallographica. Section D, Structural Biology. 75: 113-122. PMID 30821701 DOI: 10.1107/S2059798319001426  0.353
2017 Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA. Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Nature Structural & Molecular Biology. PMID 28892041 DOI: 10.1038/Nsmb.3466  0.322
2017 Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Batyuk A, Ciftci H, Guillet S, Hayes MJ, Hayes B, Lane TJ, Liang M, Lundström U, ... ... Holton JM, et al. Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin. Scientific Data. 4: 170055. PMID 28440794 DOI: 10.1038/Sdata.2017.55  0.353
2016 Hunter MS, Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Ciftci H, Guillet S, Hayes MJ, Lane TJ, Liang M, Lundström U, Koglin JE, ... ... Holton JM, et al. Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser. Nature Communications. 7: 13388. PMID 27811937 DOI: 10.1038/Ncomms13388  0.374
2016 Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Elife. 5. PMID 27731796 DOI: 10.7554/Elife.18740  0.378
2016 Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. Author response: Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex Elife. DOI: 10.7554/Elife.18740.027  0.379
2015 Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, et al. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife. 4. PMID 26422513 DOI: 10.7554/Elife.07574  0.587
2015 Rosenberg OS, Dovala D, Li X, Connolly L, Bendebury A, Finer-Moore J, Holton J, Cheng Y, Stroud RM, Cox JS. Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion. Cell. 161: 501-12. PMID 25865481 DOI: 10.1016/J.Cell.2015.03.040  0.363
2015 Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nature Methods. 12: 127-30. PMID 25532136 DOI: 10.1038/Nmeth.3212  0.392
2015 Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Benschoten AHV, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, et al. Author response: Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography Elife. DOI: 10.7554/Elife.07574.055  0.494
2014 Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, ... ... Holton JM, et al. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proceedings of the National Academy of Sciences of the United States of America. 111: 17122-7. PMID 25362050 DOI: 10.1073/Pnas.1418733111  0.398
2014 Holton JM, Classen S, Frankel KA, Tainer JA. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. The Febs Journal. 281: 4046-60. PMID 25040949 DOI: 10.1111/Febs.12922  0.331
2014 Mavrici D, Marakalala MJ, Holton JM, Prigozhin DM, Gee CL, Zhang YJ, Rubin EJ, Alber T. Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC. Proceedings of the National Academy of Sciences of the United States of America. 111: 8037-42. PMID 24843173 DOI: 10.1073/Pnas.1321812111  0.611
2014 Lang PT, Holton JM, Fraser JS, Alber T. Protein structural ensembles are revealed by redefining X-ray electron density noise Proceedings of the National Academy of Sciences of the United States of America. 111: 237-242. PMID 24363322 DOI: 10.1073/Pnas.1302823110  0.695
2014 Holton J. Promises and pitfalls of In-situ diffraction Acta Crystallographica Section a Foundations and Advances. 70: C1140-C1140. DOI: 10.1107/S2053273314088597  0.381
2013 Zeldin OB, Brockhauser S, Bremridge J, Holton JM, Garman EF. Predicting the X-ray lifetime of protein crystals. Proceedings of the National Academy of Sciences of the United States of America. 110: 20551-6. PMID 24297937 DOI: 10.1073/Pnas.1315879110  0.348
2013 White TA, Barty A, Stellato F, Holton JM, Kirian RA, Zatsepin NA, Chapman HN. Crystallographic data processing for free-electron laser sources. Acta Crystallographica. Section D, Biological Crystallography. 69: 1231-40. PMID 23793149 DOI: 10.1107/S0907444913013620  0.317
2013 Janowski PA, Cerutti DS, Holton J, Case DA. Peptide crystal simulations reveal hidden dynamics. Journal of the American Chemical Society. 135: 7938-48. PMID 23631449 DOI: 10.1021/Ja401382Y  0.344
2013 Classen S, Hura GL, Holton JM, Rambo RP, Rodic I, McGuire PJ, Dyer K, Hammel M, Meigs G, Frankel KA, Tainer JA. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. Journal of Applied Crystallography. 46: 1-13. PMID 23396808 DOI: 10.1107/S0021889812048698  0.363
2012 Aquila A, Hunter MS, Doak RB, Kirian RA, Fromme P, White TA, Andreasson J, Arnlund D, Bajt S, Barends TR, Barthelmess M, Bogan MJ, Bostedt C, Bottin H, Bozek JD, ... ... Holton JM, et al. Time-resolved protein nanocrystallography using an X-ray free-electron laser. Optics Express. 20: 2706-16. PMID 22330507 DOI: 10.1364/Oe.20.002706  0.383
2011 Lomb L, Barends TR, Kassemeyer S, Aquila A, Epp SW, Erk B, Foucar L, Hartmann R, Rudek B, Rolles D, Rudenko A, Shoeman RL, Andreasson J, Bajt S, Barthelmess M, ... ... Holton JM, et al. Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Physical Review. B, Condensed Matter and Materials Physics. 84: 214111. PMID 24089594 DOI: 10.1103/Physrevb.84.214111  0.331
2011 Fraser JS, Van Den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T. Accessing protein conformational ensembles using room-temperature X-ray crystallography Proceedings of the National Academy of Sciences of the United States of America. 108: 16247-16252. PMID 21918110 DOI: 10.1073/Pnas.1111325108  0.719
2011 Chou S, Krasileva KV, Holton JM, Steinbrenner AD, Alber T, Staskawicz BJ. Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces. Proceedings of the National Academy of Sciences of the United States of America. 108: 13323-8. PMID 21788488 DOI: 10.1073/Pnas.1109791108  0.618
2011 Spence JC, Kirian RA, Wang X, Weierstall U, Schmidt KE, White T, Barty A, Chapman HN, Marchesini S, Holton J. Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals. Optics Express. 19: 2866-73. PMID 21369108 DOI: 10.1364/Oe.19.002866  0.318
2011 Kirian RA, White TA, Holton JM, Chapman HN, Fromme P, Barty A, Lomb L, Aquila A, Maia FR, Martin AV, Fromme R, Wang X, Hunter MS, Schmidt KE, Spence JC. Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. Acta Crystallographica. Section a, Foundations of Crystallography. 67: 131-40. PMID 21325716 DOI: 10.1107/S0108767310050981  0.4
2011 Chapman HN, Fromme P, Barty A, White TA, Kirian RA, Aquila A, Hunter MS, Schulz J, DePonte DP, Weierstall U, Doak RB, Maia FR, Martin AV, Schlichting I, Lomb L, ... ... Holton JM, et al. Femtosecond X-ray protein nanocrystallography. Nature. 470: 73-7. PMID 21293373 DOI: 10.1038/Nature09750  0.422
2010 Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Science : a Publication of the Protein Society. 19: 1420-31. PMID 20499387 DOI: 10.1002/Pro.423  0.736
2010 Kirian RA, Wang X, Weierstall U, Schmidt KE, Spence JC, Hunter M, Fromme P, White T, Chapman HN, Holton J. Femtosecond protein nanocrystallography-data analysis methods. Optics Express. 18: 5713-23. PMID 20389587 DOI: 10.1364/Oe.18.005713  0.383
2010 Holton JM, Frankel KA. The minimum crystal size needed for a complete diffraction data set. Acta Crystallographica. Section D, Biological Crystallography. 66: 393-408. PMID 20382993 DOI: 10.1107/S0907444910007262  0.343
2009 Howells MR, Beetz T, Chapman HN, Cui C, Holton JM, Jacobsen CJ, Kirz J, Lima E, Marchesini S, Miao H, Sayre D, Shapiro DA, Spence JC, Starodub D. An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. Journal of Electron Spectroscopy and Related Phenomena. 170: 4-12. PMID 20463854 DOI: 10.1016/J.Elspec.2008.10.008  0.33
2009 Owen RL, Holton JM, Schulze-Briese C, Garman EF. Determination of X-ray flux using silicon pin diodes. Journal of Synchrotron Radiation. 16: 143-51. PMID 19240326 DOI: 10.1107/S0909049508040429  0.306
2009 Holton JM. A beginner's guide to radiation damage. Journal of Synchrotron Radiation. 16: 133-42. PMID 19240325 DOI: 10.1107/S0909049509004361  0.326
2009 Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W. 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins. Journal of Structural and Functional Genomics. 10: 193-208. PMID 19148774 DOI: 10.1007/S10969-008-9058-3  0.337
2008 May A, Fowler B, Frankel K, Meigs G, Holton J. Diffraction-capable microfluidic crystallization chips for screening and structure determination Acta Crystallographica Section a Foundations of Crystallography. 64: C133-C134. DOI: 10.1107/S0108767308095706  0.35
2007 Sales M, Plecs JJ, Holton JM, Alber T. Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids. Protein Science : a Publication of the Protein Society. 16: 2224-32. PMID 17766380 DOI: 10.1110/Ps.062702907  0.619
2007 Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JH. A steric block in translation caused by the antibiotic spectinomycin. Acs Chemical Biology. 2: 545-52. PMID 17696316 DOI: 10.1021/Cb700100N  0.351
2007 Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nature Structural & Molecular Biology. 14: 727-32. PMID 17660832 DOI: 10.1038/Nsmb1271  0.354
2007 Howard RJ, Clark KA, Holton JM, Minor DL. Structural insight into KCNQ (Kv7) channel assembly and channelopathy. Neuron. 53: 663-75. PMID 17329207 DOI: 10.1016/J.Neuron.2007.02.010  0.359
2007 Holton JM. XANES measurements of the rate of radiation damage to selenomethionine side chains. Journal of Synchrotron Radiation. 14: 51-72. PMID 17211072 DOI: 10.1107/S0909049506048898  0.398
2006 Rho BS, Hung LW, Holton JM, Vigil D, Kim SI, Park MS, Terwilliger TC, Pédelacq JD. Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis. Journal of Molecular Biology. 361: 850-63. PMID 16884737 DOI: 10.1016/J.Jmb.2006.05.076  0.362
2005 Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. Structures of the bacterial ribosome at 3.5 A resolution. Science (New York, N.Y.). 310: 827-34. PMID 16272117 DOI: 10.1126/Science.1117230  0.379
2005 Scott A, Chung HY, Gonciarz-Swiatek M, Hill GC, Whitby FG, Gaspar J, Holton JM, Viswanathan R, Ghaffarian S, Hill CP, Sundquist WI. Structural and mechanistic studies of VPS4 proteins. The Embo Journal. 24: 3658-69. PMID 16193069 DOI: 10.1038/Sj.Emboj.7600818  0.397
2005 Huang DT, Paydar A, Zhuang M, Waddell MB, Holton JM, Schulman BA. Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1. Molecular Cell. 17: 341-50. PMID 15694336 DOI: 10.1016/J.Molcel.2004.12.020  0.309
2004 Lopper M, Holton JM, Keck JL. Crystal structure of PriB, a component of the Escherichia coli replication restart primosome. Structure (London, England : 1993). 12: 1967-75. PMID 15530361 DOI: 10.1016/J.Str.2004.09.004  0.374
2004 MacDowell AA, Celestre RS, Howells M, McKinney W, Krupnick J, Cambie D, Domning EE, Duarte RM, Kelez N, Plate DW, Cork CW, Earnest TN, Dickert J, Meigs G, Ralston C, ... Holton JM, et al. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. Journal of Synchrotron Radiation. 11: 447-55. PMID 15496731 DOI: 10.1107/S0909049504024835  0.601
2004 Huang DT, Miller DW, Mathew R, Cassell R, Holton JM, Roussel MF, Schulman BA. A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8. Nature Structural & Molecular Biology. 11: 927-35. PMID 15361859 DOI: 10.1038/Nsmb826  0.311
2004 Sundquist WI, Schubert HL, Kelly BN, Hill GC, Holton JM, Hill CP. Ubiquitin recognition by the human TSG101 protein. Molecular Cell. 13: 783-9. PMID 15053872 DOI: 10.1016/S1097-2765(04)00129-7  0.442
2004 Holton J, Alber T. Automated protein crystal structure determination using ELVES. Proceedings of the National Academy of Sciences of the United States of America. 101: 1537-42. PMID 14752198 DOI: 10.1073/Pnas.0306241101  0.665
2003 Walden H, Podgorski MS, Huang DT, Miller DW, Howard RJ, Minor DL, Holton JM, Schulman BA. The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Molecular Cell. 12: 1427-37. PMID 14690597 DOI: 10.1016/S1097-2765(03)00452-0  0.343
2001 Crowder S, Holton J, Alber T. Covariance analysis of RNA recognition motifs identifies functionally linked amino acids Journal of Molecular Biology. 310: 793-800. PMID 11453688 DOI: 10.1006/Jmbi.2001.4740  0.576
2001 Lougheed JC, Holton JM, Alber T, Bazan JF, Handel TM. Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins. Proceedings of the National Academy of Sciences of the United States of America. 98: 5515-20. PMID 11331761 DOI: 10.1073/Pnas.091601698  0.629
2001 Rose RB, Endrizzi JA, Cronk JD, Holton J, Alber T. High-resolution structure of the HNF-1 alpha dimerization domain (vol. 39, pg. 15062, 2000) Biochemistry. 40. DOI: 10.1021/Bi0151263  0.589
2000 Rose RB, Endrizzi JA, Cronk JD, Holton J, Alber T. High-resolution structure of the HNF-1alpha dimerization domain. Biochemistry. 39: 15062-70. PMID 11106484 DOI: 10.1021/Bi001996T  0.729
2000 Glaeser R, Facciotti M, Walian P, Rouhani S, Holton J, MacDowell A, Celestre R, Cambie D, Padmore H. Characterization of conditions required for x-ray diffraction experiments with protein microcrystals Biophysical Journal. 78: 3178-3185. PMID 10827994 DOI: 10.1016/S0006-3495(00)76854-8  0.389
1999 McWhirter SM, Pullen SS, Holton JM, Crute JJ, Kehry MR, Alber T. Crystallographic analysis of CD40 recognition and signaling by human TRAF2. Proceedings of the National Academy of Sciences of the United States of America. 96: 8408-13. PMID 10411888 DOI: 10.1073/Pnas.96.15.8408  0.711
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