logo3

Newsletter No. 443
May 17, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


APRIL 2021 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Liu Q, Zhang P, Miao H, Lin Y, Kwon YD,
Kwong PD, Rikhtegaran-Tehrani Z,
Seaman MS, DeVico AL, Sajadi MM, Lusso P. Rational engraftment of quaternary-
interactive acidic loops for anti-HIV-1 antibody improvement
. J Virol. 2021 Apr
7:JVI.00159-21. doi: 10.1128/JVI.00159-21. Epub ahead of print. PMID: 33827946.

2: Guérin J, Buchanan SK. Protein import and export across the bacterial outer
membrane
. Curr Opin Struct Biol. 2021 Apr 23;69:55-62. doi:
10.1016/j.sbi.2021.03.007. Epub ahead of print. PMID: 33901701.

3: Liu H, Lu YN, Paul T, Periz G, Banco MT, Ferré-D'Amaré AR, Rothstein JD,
Hayes LR, Myong S, Wang J. A Helicase Unwinds Hexanucleotide Repeat RNA
G-Quadruplexes and Facilitates Repeat-Associated Non-AUG Translation
. J Am Chem
Soc. 2021 Apr 15. doi: 10.1021/jacs.1c00131. Epub ahead of print. PMID:
33855846.

4: Wang P, Casner RG, Nair MS, Wang M, Yu J, Cerutti G, Liu L,
Kwong PD, Huang
Y, Shapiro L, Ho DD. Increased resistance of SARS-CoV-2 variant P.1 to antibody
neutralization
. Cell Host Microbe. 2021 Apr 18:S1931-3128(21)00183-9. doi:
10.1016/j.chom.2021.04.007. Epub ahead of print. PMID: 33887205; PMCID:
PMC8053237.

5: Mukhamedova M, Wrapp D, Shen CH, Gilman MSA, Ruckwardt TJ, Schramm CA, Ault
L, Chang L, Derrien-Colemyn A, Lucas SAM, Ransier A, Darko S, Phung E, Wang L,
Zhang Y, Rush SA, Madan B, Stewart-Jones GBE, Costner PJ, Holman LA, Hickman SP,
Berkowitz NM, Doria-Rose NA, Morabito KM, DeKosky BJ, Gaudinski MR, Chen GL,
Crank MC, Misasi J, Sullivan NJ, Douek DC,
Kwong PD, Graham BS, McLellan JS,
Mascola JR. Vaccination with prefusion-stabilized respiratory syncytial virus
fusion protein induces genetically and antigenically diverse antibody responses
.
Immunity. 2021 Apr 13;54(4):769-780.e6. doi: 10.1016/j.immuni.2021.03.004. Epub
2021 Apr 5. PMID: 33823129.

6: Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH. Watching a double strand
break repair polymerase insert a pro-mutagenic oxidized nucleotide
. Nat Commun.
2021 Apr 6;12(1):2059. doi: 10.1038/s41467-021-21354-6. PMID: 33824325; PMCID:
PMC8024293.

7: Corrigan AR, Duan H, Cheng C, Gonelli CA, Ou L, Xu K, DeMouth ME, Geng H,
Narpala S, O'Connell S, Zhang B, Zhou T, Basappa M, Boyington JC, Chen SJ,
O'Dell S, Pegu A, Stephens T, Tsybovsky Y, van Schooten J, Todd JP, Wang S; VRC
Production Program, Doria-Rose NA, Foulds KE, Koup RA, McDermott AB, van Gils
MJ,
Kwong PD, Mascola JR. Fusion peptide priming reduces immune responses to
HIV-1 envelope trimer base
. Cell Rep. 2021 Apr 6;35(1):108937. doi:
10.1016/j.celrep.2021.108937. PMID: 33826898; PMCID: PMC8070658.

8: Ko SH, Bayat Mokhtari E, Mudvari P, Stein S, Stringham CD, Wagner D, Ramelli
S, Ramos-Benitez MJ, Strich JR, Davey RT Jr, Zhou T, Misasi J,
Kwong PD, Chertow
DS, Sullivan NJ, Boritz EA. High-throughput, single-copy sequencing reveals
SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute
COVID-19
. PLoS Pathog. 2021 Apr 8;17(4):e1009431. doi:
10.1371/journal.ppat.1009431. PMID: 33831133; PMCID: PMC8031304.

9: Hopp CS, Sekar P, Diouf A, Miura K, Boswell K, Skinner J, Tipton CM, Peterson
ME, Chambers MJ, Andrews S, Lu J, Tan J, Li S, Doumbo S, Kayentao K, Ongoiba A,
Traore B, Portugal S, Sun PD, Long C, Koup RA, Long EO, McDermott AB, Crompton
PD. Plasmodium falciparum-specific IgM B cells dominate in children, expand with
malaria, and produce functional IgM
. J Exp Med. 2021 Apr 5;218(4):e20200901.
doi: 10.1084/jem.20200901. PMID: 33661303; PMCID: PMC7938365.

10: Tugarinov V, Ceccon A, Clore GM. Probing Side-Chain Dynamics in Proteins by
NMR Relaxation of Isolated <sup>13</sup>C Magnetization Modes in
<sup>13</sup>CH<sub>3</sub> Methyl Groups
. J Phys Chem B. 2021 Apr
8;125(13):3343-3352. doi: 10.1021/acs.jpcb.1c00989. Epub 2021 Mar 26. PMID:
33769060.


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 - Suggestions?


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

ARCHIVE: 2005 - 2020.

 LINKS - Suggestions?

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