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Newsletter No. 445
June 14, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


MAY 2021 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Zhao G, Kosek D, Liu HB, Ohlemacher SI, Blackburne B, Nikolskaya A, Makarova
KS, Sun J, Barry Iii CE, Koonin EV, Dyda F, Bewley CA. Structural Basis for a
Dual Function ATP Grasp Ligase That Installs Single and Bicyclic ω-Ester
Macrocycles in a New Multicore RiPP Natural Product
. J Am Chem Soc. 2021 May 24.
doi: 10.1021/jacs.1c02316. Epub ahead of print. PMID: 34028251.

2: Gulla K, Cibelli N, Cooper JW, Fuller HC, Schneiderman Z, Witter S, Zhang Y,
Changela A, Geng H, Hatcher C, Narpala S, Tsybovsky Y, Zhang B, Vrc Production
Program, McDermott AB,
Kwong PD, Gowetski DB. A non-affinity purification
process for GMP production of prefusion-closed HIV-1 envelope trimers from
clades A and C for clinical evaluation
. Vaccine. 2021 May
18:S0264-410X(21)00545-4. doi: 10.1016/j.vaccine.2021.04.063. Epub ahead of
print. PMID: 34020817.

3: Mayer ML. Partial agonists go molecular. Trends Pharmacol Sci. 2021 May
6:S0165-6147(21)00078-X. doi: 10.1016/j.tips.2021.04.008. Epub ahead of print.
PMID: 33965248.

4: Zhao H, Wu D, Nguyen A, Li Y, Adão RC, Valkov E, Patterson GH, Piszczek G,
Schuck P. Energetic and structural features of SARS-CoV-2 N-protein co-
assemblies with nucleic acids
. iScience. 2021 May 7:102523. doi:
10.1016/j.isci.2021.102523. Epub ahead of print. PMID: 33997662; PMCID:
PMC8103780.

5: Williams WB, Meyerhoff RR, Edwards RJ, Li H, Manne K, Nicely NI, Henderson R,
Zhou Y, Janowska K, Mansouri K, Gobeil S, Evangelous T, Hora B, Berry M,
Abuahmad AY, Sprenz J, Deyton M, Stalls V, Kopp M, Hsu AL, Borgnia MJ, Stewart-
Jones GBE, Lee MS, Bronkema N, Moody MA, Wiehe K, Bradley T, Alam SM, Parks RJ,
Foulger A, Oguin T, Sempowski GD, Bonsignori M, LaBranche CC, Montefiori DC,
Seaman M, Santra S, Perfect J, Francica JR, Lynn GM, Aussedat B, Walkowicz WE,
Laga R, Kelsoe G, Saunders KO, Fera D,
Kwong PD, Seder RA, Bartesaghi A, Shaw
GM, Acharya P, Haynes BF. Fab-dimerized glycan-reactive antibodies are a
structural category of natural antibodies
. Cell. 2021 May
27;184(11):2955-2972.e25. doi: 10.1016/j.cell.2021.04.042. Epub 2021 May 20.
PMID: 34019795; PMCID: PMC8135257.

6: Dixit U, Bhutoria S, Wu X, Qiu L, Spira M, Mathew S, Harris R, Adams LJ,
Cahill S, Pathak R, Rajesh Kumar P, Nguyen M, Acharya SA, Brenowitz M, Almo SC,
Zou X, Steven AC, Cowburn D, Girvin M, Kalpana GV. INI1/SMARCB1 Rpt1 domain
mimics TAR RNA in binding to integrase to facilitate HIV-1 replication
. Nat
Commun. 2021 May 12;12(1):2743. doi: 10.1038/s41467-021-22733-9. PMID: 33980829;
PMCID: PMC8115288.

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


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 - 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