James M Holton

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc XANES measurements of the rate of radiation damage to selenomethionine side chains
    James M Holton
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2330, USA
    J Synchrotron Radiat 14:51-72. 2007
  2. pmc A beginner's guide to radiation damage
    James M Holton
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2330, USA
    J Synchrotron Radiat 16:133-42. 2009
  3. pmc The minimum crystal size needed for a complete diffraction data set
    James M Holton
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2330, USA
    Acta Crystallogr D Biol Crystallogr 66:393-408. 2010
  4. pmc The point-spread function of fiber-coupled area detectors
    James M Holton
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2330, USA
    J Synchrotron Radiat 19:1006-11. 2012
  5. pmc Accessing protein conformational ensembles using room-temperature X-ray crystallography
    James S Fraser
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3220, USA
    Proc Natl Acad Sci U S A 108:16247-52. 2011
  6. pmc Automated electron-density sampling reveals widespread conformational polymorphism in proteins
    P Therese Lang
    Department of Molecular and Cell Biology, University of California, Berkeley, California 97420 3220, USA
    Protein Sci 19:1420-31. 2010
  7. ncbi request reprint Suite of three protein crystallography beamlines with single superconducting bend magnet as the source
    Alastair A MacDowell
    Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    J Synchrotron Radiat 11:447-55. 2004
  8. pmc Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces
    Seemay Chou
    Department of Cell and Molecular Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 108:13323-8. 2011
  9. ncbi request reprint Structures of the bacterial ribosome at 3.5 A resolution
    Barbara S Schuwirth
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Science 310:827-34. 2005
  10. pmc Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids
    Mark Sales
    Department of Physics, University of California, Berkeley, California 94720 3206, USA
    Protein Sci 16:2224-32. 2007

Collaborators

  • James S Fraser
  • Wen Zhang
  • Alastair A MacDowell
  • Thomas Terwilliger
  • DANIEL MINOR
  • Danny T Huang
  • Maria A Borovinskaya
  • Brenda A Schulman
  • Tom Alber
  • Mark Sales
  • Barbara S Schuwirth
  • Seemay Chou
  • P Therese Lang
  • Jamie H Doudna Cate
  • Min Zhuang
  • Beom Seop Rho
  • Matthew Lopper
  • Wesley I Sundquist
  • David W Miller
  • Helen Walden
  • Ksenia V Krasileva
  • Brian J Staskawicz
  • Adam D Steinbrenner
  • Nathaniel Echols
  • Jacob E Corn
  • HO LEUNG NG
  • Raj D Pai
  • Kurt Fredrick
  • Joseph J Plecs
  • Shinichiro Shoji
  • Harold W Hunt
  • Jamie H D Cate
  • Hideko Kaji
  • Melanie D Ohi
  • Go Hirokawa
  • Akira Kaji
  • Jean Denis PĆ©delacq
  • Dominico Vigil
  • Min S Park
  • Li Wei Hung
  • Su Il Kim
  • Anton Vila-Sanjurjo
  • Amir Paydar
  • Cathy W Hau
  • M Brett Waddell
  • Gina C Hill
  • Christopher P Hill
  • Rose Mathew
  • Robert Cassell
  • Martine F Roussel
  • Brian N Kelly
  • James L Keck
  • Heidi L Schubert
  • Rebecca J Howard
  • Michael S Podgorski

Detail Information

Publications19

  1. pmc XANES measurements of the rate of radiation damage to selenomethionine side chains
    James M Holton
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2330, USA
    J Synchrotron Radiat 14:51-72. 2007
    ..This protection was found to arise from the folded structure of the protein molecule. A mechanism to explain observed decay rates involving the damaging species following the electric field lines around protein molecules is proposed...
  2. pmc A beginner's guide to radiation damage
    James M Holton
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2330, USA
    J Synchrotron Radiat 16:133-42. 2009
    ....
  3. pmc The minimum crystal size needed for a complete diffraction data set
    James M Holton
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2330, USA
    Acta Crystallogr D Biol Crystallogr 66:393-408. 2010
    ..These results suggest that reduction of background photons and diffraction spot size on the detector are the principal paths to improving crystallographic data quality beyond current limits...
  4. pmc The point-spread function of fiber-coupled area detectors
    James M Holton
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2330, USA
    J Synchrotron Radiat 19:1006-11. 2012
    ..Further analysis revealed that the tails are dominated by the fiber-optic taper, with negligible contribution from the phosphor, suggesting that the PSF of all fiber-coupled CCD-type detectors is best described as a Moffat function...
  5. pmc Accessing protein conformational ensembles using room-temperature X-ray crystallography
    James S Fraser
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3220, USA
    Proc Natl Acad Sci U S A 108:16247-52. 2011
    ..Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation...
  6. pmc Automated electron-density sampling reveals widespread conformational polymorphism in proteins
    P Therese Lang
    Department of Molecular and Cell Biology, University of California, Berkeley, California 97420 3220, USA
    Protein Sci 19:1420-31. 2010
    ..Ringer provides an objective, systematic method to identify previously undiscovered alternate conformations that can mediate protein folding and function...
  7. ncbi request reprint Suite of three protein crystallography beamlines with single superconducting bend magnet as the source
    Alastair A MacDowell
    Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    J Synchrotron Radiat 11:447-55. 2004
    ..The optical properties of the beamline are an excellent match to those required by the small protein crystals that are typically measured. The design and performance of these new beamlines are described...
  8. pmc Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces
    Seemay Chou
    Department of Cell and Molecular Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 108:13323-8. 2011
    ..These results suggest that ATR1 is a modular repeat protein belonging to an ancient family of oomycete effectors that rapidly evolves to escape host detection and adopt diverse virulence functions...
  9. ncbi request reprint Structures of the bacterial ribosome at 3.5 A resolution
    Barbara S Schuwirth
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Science 310:827-34. 2005
    ....
  10. pmc Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids
    Mark Sales
    Department of Physics, University of California, Berkeley, California 94720 3206, USA
    Protein Sci 16:2224-32. 2007
    ..These results suggest that the RH4B structure populates an unanticipated variety of structures...
  11. ncbi request reprint A steric block in translation caused by the antibiotic spectinomycin
    Maria A Borovinskaya
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    ACS Chem Biol 2:545-52. 2007
    ..These structural and biochemical data indicate that in solution spectinomycin sterically blocks swiveling of the head domain of the small ribosomal subunit and thereby disrupts the translocation cycle...
  12. ncbi request reprint Structural basis for aminoglycoside inhibition of bacterial ribosome recycling
    Maria A Borovinskaya
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nat Struct Mol Biol 14:727-32. 2007
    ..Aminoglycosides bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for aminoglycoside inhibition of ribosome recycling...
  13. pmc Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity
    Danny T Huang
    Howard Hughes Medical Institute, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Nature 445:394-8. 2007
    ..Thus, transferring the UBL's thioester linkage between successive conjugation enzymes can induce conformational changes and alter interaction networks to drive consecutive steps in UBL cascades...
  14. ncbi request reprint Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis
    Beom Seop Rho
    Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Mol Biol 361:850-63. 2006
    ..The M. tuberculosis Tpx is dimeric both in solution and in the crystal structure. Amino acid residues from both monomers delineate the active site pocket...
  15. ncbi request reprint Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1
    Danny T Huang
    Department of Structural Biology, Department of Genetics Tumor Cell Biology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Mol Cell 17:341-50. 2005
    ....
  16. ncbi request reprint Crystal structure of PriB, a component of the Escherichia coli replication restart primosome
    Matthew Lopper
    Department of Biomolecular Chemistry, University of Wisconsin Medical School, 550 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706, USA
    Structure 12:1967-75. 2004
    ..This is the first high-resolution structure of a protein involved in oriC-independent replisome loading and provides unique insight into mechanisms of replication restart in E. coli...
  17. pmc A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8
    Danny T Huang
    Department of Structural Biology, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Nat Struct Mol Biol 11:927-35. 2004
    ....
  18. ncbi request reprint Ubiquitin recognition by the human TSG101 protein
    Wesley I Sundquist
    Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA
    Mol Cell 13:783-9. 2004
    ....
  19. ncbi request reprint The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1
    Helen Walden
    Departments of Structural Biology and Genetics Tumor Cell Biology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Mol Cell 12:1427-37. 2003
    ....