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Newsletter No. 421
May 18, 2020

ACA News, IUCr Newsletter, IUCr Meetings List


APRIL 2020 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Rantalainen K, Berndsen ZT, Antanasijevic A, Schiffner T, Zhang X, Lee WH,
Torres JL, Zhang L, Irimia A, Copps J, Zhou KH, Kwon YD, Law WH, Schramm CA,
Verardi R, Krebs SJ,
Kwong PD, Doria-Rose NA, Wilson IA, Zwick MB, Yates JR 3rd,
Schief WR, Ward AB. HIV-1 Envelope and MPER Antibody Structures in Lipid
Assemblies
. Cell Rep. 2020 Apr 28;31(4):107583. doi:
10.1016/j.celrep.2020.107583. PubMed PMID: 32348769.

2: Lu J, Van Laethem F, Saba I, Chu J, Tikhonova AN, Bhattacharya A, Singer A,
Sun PD. Structure of MHC-Independent TCRs and Their Recognition of Native Antigen
CD155
. J Immunol. 2020 Apr 22. pii: ji1901084. doi: 10.4049/jimmunol.1901084.
[Epub ahead of print] PubMed PMID: 32321756.

3: Brzezinski D, Dauter Z, Minor W, Jaskolski M. On the evolution of the quality
of macromolecular models in the PDB
. FEBS J. 2020 Apr 20. doi:
10.1111/febs.15314. [Epub ahead of print] PubMed PMID: 32311227.

4: Wu W, Watts NR, Cheng N, Huang R, Steven AC, Wingfield PT. Expression of
quasi-equivalence and capsid dimorphism in the Hepadnaviridae
. PLoS Comput Biol.
2020 Apr 20;16(4):e1007782. doi: 10.1371/journal.pcbi.1007782. eCollection 2020
Apr. PubMed PMID: 32310951.

5: Chuang GY, Lai YT, Boyington JC, Cheng C, Geng H, Narpala S, Rawi R, Schmidt
SD, Tsybovsky Y, Verardi R, Xu K, Yang Y, Zhang B, Chambers M, Changela A,
Corrigan AR, Kong R, Olia AS, Ou L, Sarfo EK, Wang S, Wu W, Doria-Rose NA,
McDermott AB, Mascola JR,
Kwong PD. Development of a 3Mut-Apex-Stabilized
Envelope Trimer that Expands HIV-1 Neutralization Breadth When Used To Boost
Fusion Peptide-Directed Vaccine-Elicited Responses
. J Virol. 2020 Apr 15. pii:
JVI.00074-20. doi: 10.1128/JVI.00074-20. [Epub ahead of print] PubMed PMID:
32295908.

6: Okuno Y, Szabo A,
Clore GM. Quantitative Interpretation of Solvent
Paramagnetic Relaxation for Probing Protein-Cosolute Interactions
. J Am Chem Soc.
2020 Apr 24. doi: 10.1021/jacs.0c00747. [Epub ahead of print] PubMed PMID:
32286812.

7: Bayfield OW, Steven AC, Antson AA. Cryo-EM structure in situ reveals a
molecular switch that safeguards virus against genome loss
. Elife. 2020 Apr 14;9.
pii: e55517. doi: 10.7554/eLife.55517. [Epub ahead of print] PubMed PMID:
32286226.

8: Gorman J, Chuang GY, Lai YT, Shen CH, Boyington JC, Druz A, Geng H, Louder MK,
McKee K, Rawi R, Verardi R, Yang Y, Zhang B, Doria-Rose NA, Lin B, Moore PL,
Morris L, Shapiro L, Mascola JR,
Kwong PD. Structure of Super-Potent Antibody
CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of
Trimer-Apex Recognition
. Cell Rep. 2020 Apr 7;31(1):107488. doi:
10.1016/j.celrep.2020.03.052. PubMed PMID: 32268107.

9: Yokobori K, Miyauchi Y, Williams JG,
Negishi M. Phosphorylation of
vaccinia-related kinase 1 at threonine 386 transduces glucose stress signal in
human liver cells
. Biosci Rep. 2020 Apr 30;40(4). pii: BSR20200498. doi:
10.1042/BSR20200498. PubMed PMID: 32266931.

10: Tugarinov V, Karamanos TK,
Clore GM. Magic-Angle-Pulse Driven Separation of
Degenerate (1) H Transitions in Methyl Groups of Proteins: Application to Studies
of Methyl Axis Dynamics
. Chemphyschem. 2020 Apr 3. doi: 10.1002/cphc.202000200.
[Epub ahead of print] PubMed PMID: 32246547.

11: Ruszkowska A, Ruszkowski M, Hulewicz JP,
Dauter Z, Brown JA. Molecular
structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples
.
Nucleic Acids Res. 2020 Apr 6;48(6):3304-3314. doi: 10.1093/nar/gkz1222. PubMed
PMID: 31930330; PubMed Central PMCID: PMC7102945.

12: Gao Y, Yang W. Different mechanisms for translocation by monomeric and
hexameric helicases
. Curr Opin Struct Biol. 2020 Apr;61:25-32. doi:
10.1016/j.sbi.2019.10.003. Epub 2019 Nov 26. Review. PubMed PMID: 31783299;
PubMed Central PMCID: PMC7156327.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Contributions?

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Biophysical Methods, Sample Preparation.

TOPIC DISCUSSIONSuggestions?

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and PublicationValidation, Table 1.

READINGS AND TUTORIALS - XFEL vs microED (Link)


Methods Comparison: XFEL vs microED (2020)

DR. ZBIGNIEW DAUTER'S LECTURES AT THE NIH (2005)
 

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

           "Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage 

            with possible use of it for phasing"


LOW RESOLUTION PHASING AND REFINEMENT (2011)

 Data Collection Strategies (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

CRYSTAL CLEAR (2014)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 Understanding Biology Through Structure (2017)

 On the state of crystallography at the dawn of the electron microscopy revolution (2017)

 The Fascinating World of Crystallography (2018)

 Data science skills for referees: I biological X-ray crystallography  (2018)

Correcting the public record of biological crystallography (2019)

A Little Dictionary of Crystallography (2019)

Early history of cryo-cooling for macromolecular crystallography (2019)

 LINKS SARS-CoV-2 Related Structures (Link)

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry
                  SARS-CoV-2 Related Structures,


Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


Servers: ACHESYM,
Anisotropy, C6@C3, DaliESPript, Grade, PDBePISA, Phyre2,
             MolProbity, RestraintLib,

Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (https://mcl1.ncifcrf.gov)