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Newsletter No. 448
August 2, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


JULY 2021 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Minor W,
Jaskolski M, Martin SJ, Dauter Z. Dr. Alexander Wlodawer-celebrating
five decades of service to the structural biology community
. FEBS J. 2021
Jul;288(14):4160-4164. doi: 10.1111/febs.16064. PMID: 34286923.

2: Xu K, Wang Y, Shen CH, Chen Y, Zhang B, Liu K, Tsybovsky Y, Wang S, Farney
SK, Gorman J, Stephens T, Verardi R, Yang Y, Zhou T, Chuang GY, Lanzavecchia A,
Piccoli L,
Kwong PD. Structural basis of LAIR1 targeting by polymorphic
Plasmodium RIFINs
. Nat Commun. 2021 Jul 9;12(1):4226. doi:
10.1038/s41467-021-24291-6. PMID: 34244481; PMCID: PMC8270905.

3: Chen X, Gellert M,
Yang W. Inner workings of RAG recombinase and its
specialization for adaptive immunity
. Curr Opin Struct Biol. 2021 Jul
7;71:79-86. doi: 10.1016/j.sbi.2021.05.014. Epub ahead of print. PMID: 34245989.

4: Chao FA, Zhang Y, Byrd RA. Theoretical classification of exchange geometries
from the perspective of NMR relaxation dispersion
. J Magn Reson. 2021
Jul;328:107003. doi: 10.1016/j.jmr.2021.107003. Epub 2021 May 11. PMID:
34058714; PMCID: PMC8205974.

5: Francica JR, Flynn BJ, Foulds KE, Noe AT, Werner AP, Moore IN, Gagne M,
Johnston TS, Tucker C, Davis RL, Flach B, O'Connell S, Andrew SF, Lamb E, Flebbe
DR, Nurmukhambetova ST, Donaldson MM, Todd JM, Zhu AL, Atyeo C, Fischinger S,
Gorman MJ, Shin S, Edara VV, Floyd K, Lai L, Boyoglu-Barnum S, Van De Wetering
R, Taylor A, McCarthy E, Lecouturier V, Ruiz S, Berry C, Tibbitts T, Andersen H,
Cook A, Dodson A, Pessaint L, Van Ry A, Koutsoukos M, Gutzeit C, Teng IT, Zhou
T, Li D, Haynes BF,
Kwong PD, McDermott A, Lewis MG, Fu TM, Chicz R, van der
Most R, Corbett KS, Suthar MS, Alter G, Roederer M, Sullivan NJ, Douek DC,
Graham BS, Casimiro D, Seder RA. Protective antibodies elicited by SARS-CoV-2
spike protein vaccination are boosted in the lung after challenge in nonhuman
primates
. Sci Transl Med. 2021 Jul 27:eabi4547. doi:
10.1126/scitranslmed.abi4547. Epub ahead of print. PMID: 34315825.

6: Wang L, Zhou T, Zhang Y, Yang ES, Schramm CA, Shi W, Pegu A, Oloniniyi OK,
Henry AR, Darko S, Narpala SR, Hatcher C, Martinez DR, Tsybovsky Y, Phung E,
Abiona OM, Antia A, Cale EM, Chang LA, Choe M, Corbett KS, Davis RL, DiPiazza
AT, Gordon IJ, Helmold Hait S, Hermanus T, Kgagudi P, Laboune F, Leung K, Liu T,
Mason RD, Nazzari AF, Novik L, O'Connell S, O'Dell S, Olia AS, Schmidt SD,
Stephens T, Stringham CD, Talana CA, Teng IT, Wagner DA, Widge AT, Zhang B,
Roederer M, Ledgerwood JE, Ruckwardt TJ, Gaudinski MR, Moore PL, Doria-Rose NA,
Baric RS, Graham BS, McDermott AB, Douek DC,
Kwong PD, Mascola JR, Sullivan NJ,
Misasi J. Ultrapotent antibodies against diverse and highly transmissible SARS-
CoV-2 variants
. Science. 2021 Jul 1:eabh1766. doi: 10.1126/science.abh1766. Epub
ahead of print. PMID: 34210892.

7: Ramakrishnan S,
Stagno JR, Heinz WF, Zuo X, Yu P, Wang YX. The mechanism
driving a solid-solid phase transition in a biomacromolecular crystal
. IUCrJ.
2021 Jun 17;8(Pt 4):655-664. doi: 10.1107/S2052252521004826. PMID: 34258013;
PMCID: PMC8256710.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS - Evolving data standards for cryo-EM structures

The development of cryo-EM is directly reflected by the growth of cryo-EM strructure depositions contributed worldwide to public data archived. The archiving systems and underlying data standards supporting depostioin, annotation, release, and validation of cyro-EM stuctures and the associated metadata describing cryo-EM experiments have been developed over time to support this growth. Recently,  CL Lawson, HM Berman, and W Chiu outlined the history of these systems and described the process by which data standards had been developed. For details, please click the link.

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

DISCUSSIONSSuggestions?

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 - The Future of Structural Biology


AlphaFold DB, Great expectations - the potential impacts of AlphaFold DB (2021)
   
AlphaFold, Highly accurate protein structure prediction with AlphaFold (2021)
   
RoseTTAFold, Accurate prediction of protein structures and interactions using a three-track neural network (2021)
   
Stephen Burley, The Future of Structural Biology from a Global Perspective (2021)

 
Joachim Frank, Single-Partical Cryo-EM: Visualizing Biological Molecules in Their Native State (2021)
 

ARCHIVE: 2005 - 2020.

 LINKS - AlphaFold Protein Structure Database (Link)

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


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