Newsletter No. 452
October 4, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


Zhang J. Interplay between Host tRNAs and HIV-1: A Structural Perspective.
Viruses. 2021 Sep 13;13(9):1819. doi: 10.3390/v13091819. PMID: 34578400; PMCID:

2: Rosati M, Agarwal M, Hu X, Devasundaram S, Stellas D, Chowdhury B, Bear J,
Burns R, Donohue D, Pessaint L, Andersen H, Lewis MG, Terpos E, Dimopoulos MA,
Wlodawer A, Mullins JI, Venzon DJ, Pavlakis GN, Felber BK. Control of SARS-CoV-2
infection after Spike DNA or Spike DNA+Protein co-immunization in rhesus
. PLoS Pathog. 2021 Sep 22;17(9):e1009701. doi:
10.1371/journal.ppat.1009701. Epub ahead of print. PMID: 34551020.

3: Kumar A, Hossain RA, Yost SA, Bu W, Wang Y, Dearborn AD, Grakoui A, Cohen JI,
Marcotrigiano J. Structural insights into hepatitis C virus receptor binding and
. Nature. 2021 Sep 15. doi: 10.1038/s41586-021-03913-5. Epub ahead of
print. PMID: 34526719.

4: Stewart-Jones GBE, Gorman J, Ou L, Zhang B, Joyce MG, Yang L, Cheng C, Chuang
GY, Foulds KE, Kong WP, Olia AS, Sastry M, Shen CH, Todd JP, Tsybovsky Y,
Verardi R, Yang Y, Collins PL, Corti D, Lanzavecchia A, Scorpio DG, Mascola JR,
Buchholz UJ,
Kwong PD. Interprotomer disulfide-stabilized variants of the human
metapneumovirus fusion glycoprotein induce high titer-neutralizing responses
Proc Natl Acad Sci U S A. 2021 Sep 28;118(39):e2106196118. doi:
10.1073/pnas.2106196118. PMID: 34551978.

5: Banach BB, Cerutti G, Fahad AS, Shen CH, Oliveira De Souza M, Katsamba PS,
Tsybovsky Y, Wang P, Nair MS, Huang Y, Francino-Urdániz IM, Steiner PJ,
Gutiérrez-González M, Liu L, López Acevedo SN, Nazzari AF, Wolfe JR, Luo Y, Olia
AS, Teng IT, Yu J, Zhou T, Reddem ER, Bimela J, Pan X, Madan B, Laflin AD,
Nimrania R, Yuen KY, Whitehead TA, Ho DD,
Kwong PD, Shapiro L, DeKosky BJ.
Paired heavy- and light-chain signatures contribute to potent SARS-CoV-2
neutralization in public antibody responses
. Cell Rep. 2021 Sep 28:109771. doi:
10.1016/j.celrep.2021.109771. Epub ahead of print. PMID: 34587480; PMCID:

6: Chill JH,
Clore GM. Editorial overview - Biophysical methods: 'Seeing is
. Curr Opin Struct Biol. 2021 Sep 10:S0959-440X(21)00128-7. doi:
10.1016/j.sbi.2021.08.005. Epub ahead of print. PMID: 34518097.

7: Ahmad J, Jiang J, Boyd LF, Zeher A, Huang R, Xia D, Natarajan K, Margulies
DH. Structures of synthetic nanobody-SARS-CoV-2-receptor binding domain
complexes reveal distinct sites of interaction
. J Biol Chem. 2021 Sep 16:101202.
doi: 10.1016/j.jbc.2021.101202. Epub ahead of print. PMID: 34537245; PMCID:

8: Frazier MN, Dillard LB, Krahn JM, Perera L, Williams JG, Wilson IM, Stewart
ZD, Pillon MC, Deterding LJ, Borgnia MJ,
Stanley RE. Characterization of SARS2
Nsp15 nuclease activity reveals it's mad about U
. Nucleic Acids Res. 2021 Sep
27;49(17):10136-10149. doi: 10.1093/nar/gkab719. PMID: 34403466; PMCID:

9: Jamsen JA, Sassa A, Perera L, Shock DD, Beard WA, Wilson SH. Structural basis
for proficient oxidized ribonucleotide insertion in double strand break repair
Nat Commun. 2021 Aug 20;12(1):5055. doi: 10.1038/s41467-021-24486-x. PMID:
34417448; PMCID: PMC8379156.

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.

DISCUSSIONSHow Many More Structures Are Needed to Train AI  for
    Prediction of "Highly Accurate" 3D Structures Based on Any Sequence?

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

Google Research, "Everyone wants to do the model work, not the data work": Data Cascades in High-Stakes AI (2021)
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 - Robetta (Link), with RoseTTAFold as a new addition

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


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

Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji