James Holton, PhD

Address600 16th St
San Francisco CA 94158
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    Eliminating Critical Systematic Errors In Structural Biology With Next-Generation Simulation
    NIH/NIGMS R01GM124149Sep 1, 2017 - May 31, 2022
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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. Nat Struct Mol Biol. 2017 Sep 11. PMID: 28892041.
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    2. 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, Koglin JE, Mgbam P, Rao Y, Rendahl T, Rodriguez E, Zhang L, Wakatsuki S, Boutet S, Holton J, Hunter MS. Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin. Sci Data. 2017 Apr 25; 4:170055. PMID: 28440794.
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    3. Chiu W, Holton J, Langan P, Sauter NK, Schlichting I, Terwilliger T, Martin JL, Read RJ, Wakatsuki S. Responses to `Atomic resolution': a badly abused term in structural biology. Acta Crystallogr D Struct Biol. 2017 Apr 01; 73(Pt 4):381-383. PMID: 28375150.
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    4. 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, Mgbam P, Rao Y, Zhang L, Wakatsuki S, Holton JM, Boutet S. Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser. Nat Commun. 2016 Nov 04; 7:13388. PMID: 27811937.
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    5. 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. 2016 Oct 12; 5. PMID: 27731796.
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    6. 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 J, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife. 2015 Sep 30; 4. PMID: 26422513; PMCID: PMC4721965.
    7. 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. 2015 Apr 23; 161(3):501-512. PMID: 25865481; PMCID: PMC4409929.
    8. 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. Nat Methods. 2015 Feb; 12(2):127-30. PMID: 25532136; PMCID: PMC4312553.
    9. 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, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):17122-7. PMID: 25362050; PMCID: PMC4260607.
    10. Holton JM, Classen S, Frankel KA, Tainer JA. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J. 2014 Sep; 281(18):4046-60. PMID: 25040949; PMCID: PMC4282448.
    11. 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. Proc Natl Acad Sci U S A. 2014 Jun 03; 111(22):8037-42. PMID: 24843173; PMCID: PMC4050617.
    12. Lang PT, Holton JM, Fraser JS, Alber T. Protein structural ensembles are revealed by redefining X-ray electron density noise. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):237-42. PMID: 24363322; PMCID: PMC3890839.
    13. Zeldin OB, Brockhauser S, Bremridge J, Holton JM, Garman EF. Predicting the X-ray lifetime of protein crystals. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):20551-6. PMID: 24297937; PMCID: PMC3870734.
    14. White TA, Barty A, Stellato F, Holton JM, Kirian RA, Zatsepin NA, Chapman HN. Crystallographic data processing for free-electron laser sources. Acta Crystallogr D Biol Crystallogr. 2013 Jul; 69(Pt 7):1231-40. PMID: 23793149; PMCID: PMC3689526.
    15. 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. J Appl Crystallogr. 2013 Feb 01; 46(Pt 1):1-13. PMID: 23396808.
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    16. Holton JM, Nielsen C, Frankel KA. The point-spread function of fiber-coupled area detectors. J Synchrotron Radiat. 2012 Nov; 19(Pt 6):1006-11. PMID: 23093762; PMCID: PMC3480276.
    17. 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, Caleman C, Coppola N, Davidsson J, DePonte DP, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Fromme R, Graafsma H, Grotjohann I, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hau-Riege S, Hauser G, Hirsemann H, Holl P, Holton JM, Hömke A, Johansson L, Kimmel N, Kassemeyer S, Krasniqi F, Kühnel KU, Liang M, Lomb L, Malmerberg E, Marchesini S, Martin AV, Maia FR, Messerschmidt M, Nass K, Reich C, Neutze R, Rolles D, Rudek B, Rudenko A, Schlichting I, Schmidt C, Schmidt KE, Schulz J, Seibert MM, Shoeman RL, Sierra R, Soltau H, Starodub D, Stellato F, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Williams GJ, Weidenspointner G, Weierstall U, Wunderer C, Barty A, Spence JC, Chapman HN. Time-resolved protein nanocrystallography using an X-ray free-electron laser. Opt Express. 2012 Jan 30; 20(3):2706-16. PMID: 22330507; PMCID: PMC3413412.
    18. 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, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, Deponte DP, Doak RB, Ekeberg T, Fleckenstein H, Fromme P, Gebhardt M, Graafsma H, Gumprecht L, Hampton CY, Hartmann A, Hauser G, Hirsemann H, Holl P, Holton JM, Hunter MS, Kabsch W, Kimmel N, Kirian RA, Liang M, Maia FR, Meinhart A, Marchesini S, Martin AV, Nass K, Reich C, Schulz J, Seibert MM, Sierra R, Soltau H, Spence JC, Steinbrener J, Stellato F, Stern S, Timneanu N, Wang X, Weidenspointner G, Weierstall U, White TA, Wunderer C, Chapman HN, Ullrich J, Strüder L, Schlichting I. Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Phys Rev B Condens Matter Mater Phys. 2011 Dec 01; 84(21):214111. PMID: 24089594.
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    19. 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. Proc Natl Acad Sci U S A. 2011 Sep 27; 108(39):16247-52. PMID: 21918110; PMCID: PMC3182744.
    20. Chou S, Krasileva KV, Holton JM, Steinbrenner AD, Alber T, Staskawicz BJ. Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces. Proc Natl Acad Sci U S A. 2011 Aug 09; 108(32):13323-8. PMID: 21788488; PMCID: PMC3156156.
    21. 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 Crystallogr A. 2011 Mar; 67(Pt 2):131-40. PMID: 21325716; PMCID: PMC3066792.
    22. 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. Opt Express. 2011 Feb 14; 19(4):2866-73. PMID: 21369108.
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    23. 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, Coppola N, Shoeman RL, Epp SW, Hartmann R, Rolles D, Rudenko A, Foucar L, Kimmel N, Weidenspointner G, Holl P, Liang M, Barthelmess M, Caleman C, Boutet S, Bogan MJ, Krzywinski J, Bostedt C, Bajt S, Gumprecht L, Rudek B, Erk B, Schmidt C, Hömke A, Reich C, Pietschner D, Strüder L, Hauser G, Gorke H, Ullrich J, Herrmann S, Schaller G, Schopper F, Soltau H, Kühnel KU, Messerschmidt M, Bozek JD, Hau-Riege SP, Frank M, Hampton CY, Sierra RG, Starodub D, Williams GJ, Hajdu J, Timneanu N, Seibert MM, Andreasson J, Rocker A, Jönsson O, Svenda M, Stern S, Nass K, Andritschke R, Schröter CD, Krasniqi F, Bott M, Schmidt KE, Wang X, Grotjohann I, Holton JM, Barends TR, Neutze R, Marchesini S, Fromme R, Schorb S, Rupp D, Adolph M, Gorkhover T, Andersson I, Hirsemann H, Potdevin G, Graafsma H, Nilsson B, Spence JC. Femtosecond X-ray protein nanocrystallography. Nature. 2011 Feb 03; 470(7332):73-7. PMID: 21293373; PMCID: PMC3429598.
    24. Classen S, Rodic I, Holton J, Hura GL, Hammel M, Tainer JA. Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system. J Synchrotron Radiat. 2010 Nov; 17(6):774-81. PMID: 20975223; PMCID: PMC2964114.
    25. 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 Sci. 2010 Jul; 19(7):1420-31. PMID: 20499387; PMCID: PMC2974833.
    26. Holton JM, Frankel KA. The minimum crystal size needed for a complete diffraction data set. Acta Crystallogr D Biol Crystallogr. 2010 Apr; 66(Pt 4):393-408. PMID: 20382993; PMCID: PMC2852304.
    27. 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. Opt Express. 2010 Mar 15; 18(6):5713-23. PMID: 20389587; PMCID: PMC4038330.
    28. 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. J Electron Spectros Relat Phenomena. 2009 Mar 01; 170(1-3):4-12. PMID: 20463854.
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    29. Owen RL, Holton JM, Schulze-Briese C, Garman EF. Determination of X-ray flux using silicon pin diodes. J Synchrotron Radiat. 2009 Mar; 16(Pt 2):143-51. PMID: 19240326; PMCID: PMC2651761.
    30. Holton JM. A beginner's guide to radiation damage. J Synchrotron Radiat. 2009 Mar; 16(Pt 2):133-42. PMID: 19240325; PMCID: PMC2651760.
    31. 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. J Struct Funct Genomics. 2009 Apr; 10(2):193-208. PMID: 19148774; PMCID: PMC2705707.
    32. Berndsen CE, Tsubota T, Lindner SE, Lee S, Holton JM, Kaufman PD, Keck JL, Denu JM. Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. Nat Struct Mol Biol. 2008 Sep; 15(9):948-56. PMID: 19172748; PMCID: PMC2678805.
    33. Sales M, Plecs JJ, Holton JM, Alber T. Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids. Protein Sci. 2007 Oct; 16(10):2224-32. PMID: 17766380; PMCID: PMC2204136.
    34. Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JH. A steric block in translation caused by the antibiotic spectinomycin. ACS Chem Biol. 2007 Aug 17; 2(8):545-52. PMID: 17696316; PMCID: PMC4624401.
    35. 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. Nat Struct Mol Biol. 2007 Aug; 14(8):727-32. PMID: 17660832.
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    36. Howard RJ, Clark KA, Holton JM, Minor DL. Structural insight into KCNQ (Kv7) channel assembly and channelopathy. Neuron. 2007 Mar 01; 53(5):663-75. PMID: 17329207; PMCID: PMC3011230.
    37. Huang DT, Hunt HW, Zhuang M, Ohi MD, Holton JM, Schulman BA. Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature. 2007 Jan 25; 445(7126):394-8. PMID: 17220875; PMCID: PMC2821831.
    38. Holton JM. XANES measurements of the rate of radiation damage to selenomethionine side chains. J Synchrotron Radiat. 2007 Jan; 14(Pt 1):51-72. PMID: 17211072; PMCID: PMC2806430.
    39. 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. J Mol Biol. 2006 Sep 01; 361(5):850-63. PMID: 16884737.
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    40. 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. 2005 Nov 04; 310(5749):827-34. PMID: 16272117.
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    41. 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. EMBO J. 2005 Oct 19; 24(20):3658-69. PMID: 16193069; PMCID: PMC1276703.
    42. 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. Mol Cell. 2005 Feb 04; 17(3):341-50. PMID: 15694336.
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    43. Lopper M, Holton JM, Keck JL. Crystal structure of PriB, a component of the Escherichia coli replication restart primosome. Structure. 2004 Nov; 12(11):1967-75. PMID: 15530361.
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    44. 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, Alber T, Berger JM, Agard DA, Padmore HA. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. J Synchrotron Radiat. 2004 Nov 01; 11(Pt 6):447-55. PMID: 15496731.
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    45. 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. Nat Struct Mol Biol. 2004 Oct; 11(10):927-35. PMID: 15361859; PMCID: PMC2862556.
    46. Sundquist WI, Schubert HL, Kelly BN, Hill GC, Holton JM, Hill CP. Ubiquitin recognition by the human TSG101 protein. Mol Cell. 2004 Mar 26; 13(6):783-9. PMID: 15053872.
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    47. Holton J, Alber T. Automated protein crystal structure determination using ELVES. Proc Natl Acad Sci U S A. 2004 Feb 10; 101(6):1537-42. PMID: 14752198; PMCID: PMC341770.
    48. 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. Mol Cell. 2003 Dec; 12(6):1427-37. PMID: 14690597.
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    49. Crowder S, Holton J, Alber T. Covariance analysis of RNA recognition motifs identifies functionally linked amino acids. J Mol Biol. 2001 Jul 20; 310(4):793-800. PMID: 11453688.
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    50. 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. Proc Natl Acad Sci U S A. 2001 May 08; 98(10):5515-20. PMID: 11331761; PMCID: PMC33244.
    51. Rose RB, Endrizzi JA, Cronk JD, Holton J, Alber T. High-resolution structure of the HNF-1alpha dimerization domain. Biochemistry. 2000 Dec 12; 39(49):15062-70. PMID: 11106484.
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    52. 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. Biophys J. 2000 Jun; 78(6):3178-85. PMID: 10827994; PMCID: PMC1300899.
    53. McWhirter SM, Pullen SS, Holton JM, Crute JJ, Kehry MR, Alber T. Crystallographic analysis of CD40 recognition and signaling by human TRAF2. Proc Natl Acad Sci U S A. 1999 Jul 20; 96(15):8408-13. PMID: 10411888; PMCID: PMC17529.
    54. Morgan CS, Holton JM, Olafson BD, Bjorkman PJ, Mayo SL. Circular dichroism determination of class I MHC-peptide equilibrium dissociation constants. Protein Sci. 1997 Aug; 6(8):1771-3. PMID: 9260291; PMCID: PMC2143769.
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