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.

2019 Publications

  1. "Structure and Molecular Recognition Mechanism of IMP-13 Metallo-Beta-Lactamase" -
    Charlotte A. Softley et al.; Antimicrobial Agents and Chemotherapy June 2020; volume 64, issue 6, e00123-20

2018 Publications

  1. "Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans" -
    Jones A.J., Hevener K.E.; Biochemical and Biophysical Research Communications 516, Issue 2, 2019, 333-338
  2. "Encoding of Promiscuity in an Aminoglycoside Acetyltransferase" -
    Prashasti Kumar, Brinda Selvaraj, Engin H. Serpersu, and Matthew J. Cuneo; J. Med. Chem. 61, 2018, 10218-10227
  3. "Structural characterization of an activin class ternary receptor complex reveals a third paradigm for receptor specificity" -
    Erich J. Goebel, Richard A. Corpina, Cynthia S. Hinck, Magdalena Czepnik, Roselyne Castonguay, Rosa Grenha, Angela Boisvert, Gabriella Miklossy, Paul T. Fullerton, Martin M. Matzuk, Vincent J. Idone, Aris N. Economides, Ravindra Kumar, Andrew P. Hinck, and Thomas B. Thompson; PNAS 116(31), 2019, 15506-15513

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
  2. "The structure of Acinetobacter secreted protease CpaA complexed with its chaperone CpaB reveals a novel mode of a T2SS chaperone-substrate interaction" -
    Urusova D.V. et al.; Journal of Biological Chemistry (2019) RA119.009805
  3. "Crosslinking of nucleotide binding domains improves the coupling efficiency of an ABC transporter" -
    Chengcheng Fan, Jens T. Kaiser, Douglas C. Rees;
  4. "Crystal Structure of a Tetrameric DNA Fold-Back Quadruplex" -
    Betty Chu, Daoning Zhang, Wonseok Hwang, and Paul J. Paukstelis; J. Am. Chem. Soc. 140 (2018) 16291-16298.
  5. "A structural framework for unidirectional transport by a bacterial ABC exporter" -
    Chengcheng Fan, Jens T. Kaiser and Douglas C. Rees; PNAS July 2020

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
  4. "tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay" -
    Peschek J. & Walter P.; eLife 2019;8:e44199
  5. "How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation" -
    Ruckthong al.; Chemistry 2019 May 10; 25(27): 6773-6787
  6. "Bidirectional modulation of HIF-2 activity through chemical ligands" -
    Wu al.; Nature Chemical Biology 15, 367-376 (2019)
  7. "Heteromeric three-stranded coiled coils designed using a Pb(II)(Cys)3 template mediated strategy" -
    Tolbert al.; Nature Chemistry 12, 405-411 (2020)
  8. "Structural characterization of three noncanonical NTF2-like superfamily proteins: implications for polyketide biosynthesis" -
    N. Vuksanovic et al.; Acta Cryst. F76, 372-383 (2020)

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)
  10. "Activation loop dynamics are controlled by conformation-selective inhibitors of ERK2" -
    Pegram L.M. et al.; PNAS 116 (31) 15463-15468 (2019)

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)
  5. "Structure of GTP cyclo hydrolase I from Listeria monocytogenes, a potential anti-infective drug target" -
    Sonja Schussler, et al.; Acta Cryst. 2019; F75 586-592

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