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Newsletter No. 446
July 12, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


JUNE 2021 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Lubkowski J, Wlodawer A. Structural and biochemical properties of
L-asparaginase
. FEBS J. 2021 Jun 1. doi: 10.1111/febs.16042. Epub ahead of
print. PMID: 34060231.

2: Ceccon A, Tugarinov V, Clore GM. Quantitative Exchange NMR-Based Analysis of
Huntingtin-SH3 Interactions Suggests an Allosteric Mechanism of Inhibition of
Huntingtin Aggregation
. J Am Chem Soc. 2021 Jun 30;143(25):9672-9681. doi:
10.1021/jacs.1c04786. Epub 2021 Jun 17. PMID: 34137596.

3: Xu J, Xu K, Jung S, Conte A, Lieberman J, Muecksch F, Lorenzi JCC, Park S,
Schmidt F, Wang Z, Huang Y, Luo Y, Nair MS, Wang P, Schulz JE, Tessarollo L,
Bylund T, Chuang GY, Olia AS, Stephens T, Teng IT, Tsybovsky Y, Zhou T, Munster
V, Ho DD, Hatziioannou T, Bieniasz PD, Nussenzweig MC,
Kwong PD, Casellas R.
Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature.
2021 Jul;595(7866):278-282. doi: 10.1038/s41586-021-03676-z. Epub 2021 Jun 7.
PMID: 34098567.

4: Naskręcki B, Dauter Z, Jaskolski M. A topological proof of the modified Euler
characteristic based on the orbifold concept
. Acta Crystallogr A Found Adv. 2021
Jul 1;77(Pt 4):317-326. doi: 10.1107/S2053273321004320. Epub 2021 Jun 21. PMID:
34196293.

5: Li D, Edwards RJ, Manne K, Martinez DR, Schäfer A, Alam SM, Wiehe K, Lu X,
Parks R, Sutherland LL, Oguin TH 3rd, McDanal C, Perez LG, Mansouri K, Gobeil
SMC, Janowska K, Stalls V, Kopp M, Cai F, Lee E, Foulger A, Hernandez GE,
Sanzone A, Tilahun K, Jiang C, Tse LV, Bock KW, Minai M, Nagata BM, Cronin K,
Gee-Lai V, Deyton M, Barr M, Von Holle T, Macintyre AN, Stover E, Feldman J,
Hauser BM, Caradonna TM, Scobey TD, Rountree W, Wang Y, Moody MA, Cain DW,
DeMarco CT, Denny TN, Woods CW, Petzold EW, Schmidt AG, Teng IT, Zhou T, Kwong
PD
, Mascola JR, Graham BS, Moore IN, Seder R, Andersen H, Lewis MG, Montefiori
DC, Sempowski GD, Baric RS, Acharya P, Haynes BF, Saunders KO. In vitro and
in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies
.
Cell. 2021 Jun 18:S0092-8674(21)00756-X. doi: 10.1016/j.cell.2021.06.021. Epub
ahead of print. PMID: 34242577; PMCID: PMC8232969.

6: Ramakrishnan S, Stagno JR, Magidson V, Heinz WF, Wang YX. Dependence of phase
transition uniformity on crystal sizes characterized using birefringence
. Struct
Dyn. 2021 Jun 30;8(3):034301. doi: 10.1063/4.0000098. PMID: 34235229; PMCID:
PMC8248999.

7: Vaisman A, Łazowski K, Reijns MAM, Walsh E, McDonald JP, Moreno KC, Quiros
DR, Schmidt M, Kranz H, Yang W, Makiela-Dzbenska K, Woodgate R. Novel
Escherichia coli active site dnaE alleles with altered base and sugar
selectivity
. Mol Microbiol. 2021 Jun 28. doi: 10.1111/mmi.14779. Epub ahead of
print. PMID: 34181784.

8: Hou S, Lee JM, Myint W, Matsuo H, Yilmaz NK, Schiffer CA. Structural basis of
substrate specificity in human cytidine deaminase family APOBEC3s
. J Biol Chem.
2021 Jun 22:100909. doi: 10.1016/j.jbc.2021.100909. Epub ahead of print. PMID:
34171358.

9: Zhou BR, Bai Y. Preparation of scFv stabilized chromatosomes for single-
particle cryo-EM structure determination
. STAR Protoc. 2021 Mar 20;2(2):100396.
doi: 10.1016/j.xpro.2021.100396. PMID: 33786462; PMCID: PMC7994535.

10: Bermek O, Williams RS. The three-component helicase/primase complex of
herpes simplex virus-1
. Open Biol. 2021 Jun;11(6):210011. doi:
10.1098/rsob.210011. Epub 2021 Jun 9. PMID: 34102080; PMCID: PMC8187027.

11: Do Kwon Y, Wang XE, Bender MF, Yang R, Li Y, McKee K, Rawi R, O'Dell S,
Schneck NA, Shaddeau A, Zhang B, Arnold FJ, Connors M, Doria-Rose NA,
Kwong PD,
Lei QP. Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic
Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography
. Antibodies
(Basel). 2021 Jun 10;10(2):23. doi: 10.3390/antib10020023. PMID: 34200826.

12: Wälti MA, Kotler SA, Clore GM. Probing the Interaction of Huntingtin Exon-1
Polypeptides with the Chaperonin Nanomachine GroEL
. Chembiochem. 2021 Jun
2;22(11):1985-1991. doi: 10.1002/cbic.202100055. Epub 2021 Apr 7. PMID:
33644966.

13: Ramakrishnan S,
Stagno JR, Magidson V, Heinz WF, Wang YX. A combined
approach to characterize ligand-induced solid-solid phase transitions in
biomacromolecular crystals
. J Appl Crystallogr. 2021 May 9;54(Pt 3):787-796.
doi: 10.1107/S1600576721003137. PMID: 34194289; PMCID: PMC8202036.

14: Fashe M, Yi M, Sueyoshi T, Negishi M. Sex-specific expression mechanism of
hepatic estrogen inactivating enzyme and transporters in diabetic women
. Biochem
Pharmacol. 2021 Jun 23;190:114662. doi: 10.1016/j.bcp.2021.114662. Epub ahead of
print. PMID: 34157297.

15: Gregory MT, Gao Y, Cui Q,
Yang W. Multiple deprotonation paths of the
nucleophile 3'-OH in the DNA synthesis reaction
. Proc Natl Acad Sci U S A. 2021
Jun 8;118(23):e2103990118. doi: 10.1073/pnas.2103990118. PMID: 34088846; PMCID:
PMC8201771.

16: Cerutti G, Rapp M, Guo Y, Bahna F, Bimela J, Reddem ER, Yu J, Wang P, Liu L,
Huang Y, Ho DD,
Kwong PD, Sheng Z, Shapiro L. Structural basis for accommodation
of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing
antibodies
. Structure. 2021 Jul 1;29(7):655-663.e4. doi:
10.1016/j.str.2021.05.014. Epub 2021 Jun 9. PMID: 34111408; PMCID: PMC8188728.

17: Adams O, Deme JC, Parker JL; CRyPTIC Consortium, Fowler PW, Lea SM, Newstead
S. Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An
emergent therapeutic target
. Structure. 2021 Jun 28:S0969-2126(21)00217-3. doi:
10.1016/j.str.2021.06.013. Epub ahead of print. PMID: 34242558.

18: Newman JD, Russell MM, Fan L, Wang YX, Gonzalez-Gutierrez G, van Kessel JC.
The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is
flexible and binds diverse DNA sequences
. Nucleic Acids Res. 2021 Jun
4;49(10):5967-5984. doi: 10.1093/nar/gkab387. PMID: 34023896; PMCID: PMC8191795.

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