Collaborative Computational Project No. 4
Software for Macromolecular X-Ray Crystallography

CCP4/APS School in Macromolecular Crystallography: From data collection to structure refinement and beyond

Publications citing work carried out at the CCP4/APS school

This page lists some of the publications where the research involved benefited from the assistance given at the CCP4/APS school. We are grateful to each of the authors for acknowledging the help they recieved at the school.

2017 Publications

  1. "ADP-Dependent Kinases From the Archaeal Order Methanosarcinales Adapt to Salt by a Non-canonical Evolutionarily Conserved Strategy" -
    Gonzalez-Ordenes Felipe, Cea Pablo A., Fuentes-Ugarte Nicolas, Munoz Sebastian M., Zamora Ricardo A., Leonardo Diego, Garratt Richard C., Castro-Fernandez Victor, Guixe Victoria (2018). Frontiers in Microbiology 9, 1305

2016 Publications

  1. "A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model" -
    Skubak, P., Arac, D., Bowler, M. W., Correia, A. R., Hoelz, A., Larsen, S., Leonard, G. A., McCarthy, A. A., McSweeney, S., Mueller-Dieckmann, C., Otten, H., Salzman, G., Pannu, N. S. (2018). IUCrJ 5, 166-171
  2. "Structural and functional analysis of mRNA export regulation by the nuclear pore complex" -
    Daniel H. Lin, Ana R. Correia, Sarah W. Cai, Ferdinand M. Huber, Claudia A. Jette, Andre Hoelz. Nature Communications 9:2319 (2018)
  3. "SIMBAD: a sequence-independent molecular-replacement pipeline" -
    Simpkin A.J. et al.; Acta Cryst. (2018); D74, Part 7, 595-605

2015 Publications

  1. "Functional consequences of B-repeat sequence variation in the Staphylococcal biofilm protein Aap: Deciphering the assembly code" -
    C. L. Shelton, D. G. Conrady, A. B. Herr; Biochemical Journal 474 (3) 427-443 (2016)
  2. "Crystal structure of a substrate-engaged SecY protein-translocation channel" -
    Long Li, Eunyong Park, JingJing Ling, Jessica Ingram, Hidde Ploegh and Tom A. Rapoport; Nature 531, 395-399 (2016)
  3. "Structure of a fungal form of aspartate semi aldehyde de hydrogenase from Cryptococcus neoformans" -
    Dahal, G. and Viola, R.E.; Acta Cryst. 2015; F71, 1365-1371
  4. "Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine Β-Lactamases by Relieving Steric Strain" -
    Stojanoski, V. et al.; Biochemistry 2016 55 (17), pp 2479-2490
  5. "Structure of the catalytic domain of the colistin resistance enzyme MCR-1" -
    Stojanoski, V. et al.; BMC Biology 2016 14:81
  6. "Crystallographic Structure of Truncated CCL21 and the Putative Sulfotyrosine-Binding Site" -
    Smith, E.W., et al.; Biochemistry 2016 55 (40), pp 5746-5753
  7. "Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5" -
    Mitchell A.J., Zhu Q., Maggiolo A.O., Ananth N.R., Hillwig M.L., Liu X., Boal A.K.; Nature Chemical Biology 12, 636-640 (2016)
  8. "EGFR Ligands Differentially Stabilize Receptor Dimers to Specify Signaling Kinetics" -
    Freed D.M., et al.; Cell 171, 1-13 (2017)
  9. "Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on V9V2 T cell activation" -
    Siui Gu et al.; PNAS 114 (35) E7311-E7320 (2017)

2014 Publications

  1. "Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative" -
    I. Mir-Sanchis, C. A. Roman, A. Misiura, Y. Z. Pigli, S. Boyle-Vavra, P. A. Rice; Nature Structural and Molecular Biology 23, 891-898 (2016).
  2. "STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability." -
    Gres AT, Kirby KA, KewalRamani VN, Tanner JJ, Pornillos O, Sarafianos SG. Science 349(6243), 99-103 (2015).
  3. "Structural basis for selective targeting of leishmanial ribosomes: aminoglycoside derivatives as promising therapeutics" -
    Shalev, M. et al.; Nucleic Acids Res., 43(17):8601-8613. 2015 Sep 30.
  4. "Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation" -
    Dobosz-Bartoszek M., et al.; Nature Communications 7:12941 (2016).
  5. "NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors" -
    Dalei Wu., et al.; eLIFE 2016;5:e18790
  6. "An elastic element in the protocadherin-15 tip link of the inner ear" -
    Araya-Secchi, R., et al.; Nature Communications 7:13458 (2016).
  7. "The PDB_REDO server for macromolecular structure model optimization" -
    Joosten R.P. et al.; IUCrJ 2014; Vol. 1, Part 4, 213-220
  8. "The crystal structure of human GlnRS provides basis for the development of neurological disorders" -
    Ognjenovic J, Wu J, Matthies D, Baxa U, Subramaniam S, Ling J, Simonovic M.; Nucleic Acids Res., 44(7):3420-3431. 2016 April 20.
  9. "A retractable lid in lecithin:cholesterol acyltransferase provides a structural mechanism for activation by apolipoprotein A-I" -
    Kelly A. et al.; J. Biol. Chem. 2017 292: 20313-

2013 Publications

  1. "Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain" -
    Jessica F. Bruhn, Katherine C. Barnett, Jaclyn Bibby, Jens M. H. Thomas, Ronan M. Keegan, Daniel J. Rigden, Zachary A. Bornholdt and Erica Ollmann Saphire J. Virol. 88 (1), 758-762 (2014).
  2. "Dimeric Structure of Pseudokinase RNase L Bound to 2-5A Reveals a Basis for Interferon-Induced Antiviral Activity" -
    Hao Huang et al., Molecular Cell 53 (2), 221-234 (2014).
  3. "Crystallization and preliminary X-ray diffraction analysis of Hypocrea jecorina Cel7A in two new crystal forms" -
    Bodenheimer A. et al.; Acta Cryst. 2014; F70, 773-776
  4. "A Distinct MaoC-like Enoyl-CoA Hydratase Architecture Mediates Cholesterol Catabolism in Mycobacterium tuberculosis" -
    Yang M. et al.; ACS Chem. Biol. 2014, 9 (11), pp 2632-2645
  5. "Targeting γ-Herpesvirus 68 Bcl-2-mediated Down-regulation of Autophagy" -
    Su, M. et al.; J. Biol. Chem. 289, 8029-8040 (2013).
  6. "Development and Structural Analysis of a Nanomolar Cyclic Peptide Antagonist for the EphA4 Receptor" -
    Lamberto, I. et al.; ACS Chem. Biol. 2014, 9 (12), pp 2787-2795
  7. "Structural insights into the binding of the human receptor for advanced glycation end products (RAGE) by S100B, as revealed by an S100B-RAGE-derived peptide complex" -
    Jenson J.L. et al.; Acta Cryst. 2015; D71, Part 5, 1176-1183
  8. "Identification of the allosteric site for neutral amino acids in the maize C4-isozyme of phosphoenolpyruvate carboxylase: The critical role of Ser100" -
    Gonzalez-Segura L. et al.; J. Biol. Chem. May, 2018

2012 Publications

  1. "In Human Pseudouridine Synthase 1 (hPus1), a C-Terminal Helical Insert Blocks tRNA from Binding in the Same Orientation as in the Pus1 Bacterial Homologue TruA, Consistent with Their Different Target Selectivities" -
    Czudnochowski N., Liya Wang A., Finer-Moore J., Stroud R.M.; J. Mol. Biol. 425 (20), 3875-3887 (2013).
  2. "Structural Basis for Enhanced HIV-1 Neutralization by a Dimeric Immunoglobulin G Form of the Glycan-Recognizing Antibody 2G12" -
    Yunji Wu, Anthony P. West, Jr., Helen J. Kim, Matthew E. Thornton, Andrew B. Ward and Pamela J. Bjorkman; Cell Reports 5, 1443-1455 (2013).
  3. "Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity" -
    Rajagopalan S., Teter S.J., Zwart P.H., Brennan R.G., Phillips K.J., Kiley P.J.; Nature Structural & Molecular Biology 20, 740-747 (2013).
  4. "Structural basis for action by diverse antidepressants on biogenic amine transporters" -
    Hui Wang, April Goehring, Kevin H. Wang, Aravind Penmatsa, Ryan Ressler and Eric Gouaux; Nature 503, 141-145 (2013).
  5. "A Mimivirus Enzyme that Participates in Viral Entry" -
    Klose, M. et al.; Structure. 2015 Jun 2;23(6):1058-1065
  6. "Structure of the apo anti-influenza CH65 Fab" -
    Peter S. Lee, Ashley J. Arnell and Ian A. Wilson; Acta Cryst. 2015; F71(2), 145-148
  7. "Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus" -
    Lee, P.S. et al.; Nature Communications 5:3614 (2014).
  8. "Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation" -
    Kim J.J., et al.; Structure 24:5 p710-720 (2016).
  9. "First attempts to crystallize a non-homogeneous sample of thioredoxin from Litopenaeus vannamei: What to do when you have diffraction data of a protein that is not the target?" -
    Campos-Acevedoa, A.A., et al.; Biochemistry and Biophysics Reports 2016 (8), pp 284-289

2011 Publications

  1. "Allosteric competitive inactivation of hematopoietic CSF-1 signaling by the viral decoy receptor BARF1" -
    Elegheert J. et al.; Nature Structural & Molecular Biology 19, 938-947 (2012)
  2. "Structural Basis of Transcription Initiation" -
    Zhang Y. et al.; Science 2012; 336, 1076
  3. "Disruption of Hydrogen Bonds between Major Histocompatibility Complex Class II and the Peptide N-Terminus Is Not Sufficient to Form a Human Leukocyte Antigen-DM Receptive State of Major Histocompatibility Complex Class II" -
    Schulze M-SED, Anders A-K, Sethi DK, Call MJ; PLoS One 2013 Jul 25; 8(7): e69228
  4. "Novel Pyridazinone Inhibitors for Vascular Adhesion Protein-1 (VAP-1): Old Target-New Inhibition Mode" -
    Bligt-Linden E. et al.; J. Med. Chem., 2013, 56 (24), pp 9837-9848
  5. "The energy landscape of adenylate kinase during catalysis" -
    Kerns SJ. et al.; Nature Structural & Molecular Biology 22(2), 123-31 (2015)
  6. "Structural Basis for Telomerase RNA Recognition and RNP Assembly by the Holoenzyme La Family Protein p65" -
    Singh, M et al.; Molecular Cell 47, 16-26 July 2012.
  7. "Crystal Structures of Aureochrome1 LOV Suggest New Design Strategies for Optogenetics" -
    Klose, M. et al.; Structure 2012 April 4;20(4):698-706
  8. "Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy" -
    Mei, Y. et al.; Biochemistry 2016 55 (13), pp 1945-1958

2010 Publications

  1. "Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein" -
    Sippel KH et al.; Proteins 2011 Feb; 79(2):528-36
  2. "Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation" -
    Nelersa, C.M., Schmier, B.J., Malhotra, A.; Acta Cryst. 2011; F67, 1235-1238
  3. "Conservation of Lipid Functions in Cytochrome bc Complexes" -
    Saif Hasan, S., Yamashita, E., Ryan, C.M., Whitelegge, J.P., Cramer, W.A.; J. of Mol. Biol. 2011; 414:145-162
  4. "Identification and characterization of a bacterial hydrosulphide ion channel" -
    Bryan K. Czyzewski & Da-Neng Wang; Nature 483, 494-497 (22 March 2012)

2009 Publications

  1. "Architecture of the Mediator head module" -
    Tsuyoshi Imasaki et al.; Nature 475, 240-243 (14 July 2011)
  2. "Validation of crystallographic models containing TLS or other descriptions of anisotropy"
    F. Zucker, P. Christoph C. and E. A Merritt; Acta Crystallographica Section D. 66 889-900 2010
  3. "Riboswitch structure: an internal residue mimicking the purine ligand" -
    Delfosse V. et al.; Nucleic Acids Res., 38(6):2057-68. Epub 2009 Dec 18
  4. "Degradation of human hemoglobin by organic C-nitroso compounds" -
    Yi J., Guan Y., Thomas L.M. and Richter-Addo G.B.; Chemical Communications, 49:11179-11181. 2013 Oct 17
  5. "The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins" -
    M. J. Feige. et al.; PNAS, 2014 111 (22) 8155-8160

2008 Publications

  1. "Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247" -
    Kirby K.A.,et al.; FASEB J. 2014 Oct 28
  2. "The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteria" -
    Aksyuk AA et al.; EMBO J. 2009 Apr 8;28(7):821-9. Epub 2009 Feb 19
  3. "The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate" -
    Aksyuk AA et al.; Structure. 2009 Jun 10;17(6):800-8
  4. "The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences" -
    Loughlin FE et al.; Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5581-6. Epub 2009 Mar 20