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Newsletter No. 455
November 15, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


OCTOBER 2021 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Yokobori K, Kawasaki Y, Sekine Y, Nobusawa S, Sakaki T, Negishi M, Kakizaki
S. Androgen receptor phosphorylated at Ser815: the expression and function in
the prostate and tumor-derived cells
. Biochem Pharmacol. 2021 Oct 26:114794.
doi: 10.1016/j.bcp.2021.114794. Epub ahead of print. PMID: 34715066.

2: Trachman RJ 3rd, Ferré-D'Amaré AR. An uncommon
[K<sup>+</sup>(Mg<sup>2+</sup>)<sub>2</sub>] metal ion triad imparts stability
and selectivity to the Guanidine-I riboswitch
. RNA. 2021 Oct;27(10):1257-1264.
doi: 10.1261/rna.078824.121. Epub 2021 Jul 13. PMID: 34257148; PMCID:
PMC8457001.

3: Dussupt V, Sankhala RS, Mendez-Rivera L, Townsley SM, Schmidt F, Wieczorek L,
Lal KG, Donofrio GC, Tran U, Jackson ND, Zaky WI, Zemil M, Tritsch SR, Chen WH,
Martinez EJ, Ahmed A, Choe M, Chang WC, Hajduczki A, Jian N, Peterson CE, Rees
PA, Rutkowska M, Slike BM, Selverian CN, Swafford I, Teng IT, Thomas PV, Zhou T,
Smith CJ, Currier JR,
Kwong PD, Rolland M, Davidson E, Doranz BJ, Mores CN,
Hatziioannou T, Reiley WW, Bieniasz PD, Paquin-Proulx D, Gromowski GD, Polonis
VR, Michael NL, Modjarrad K, Joyce MG, Krebs SJ. Low-dose in vivo protection and
neutralization across SARS-CoV-2 variants by monoclonal antibody combinations
.
Nat Immunol. 2021 Oct 29. doi: 10.1038/s41590-021-01068-z. Epub ahead of print.
PMID: 34716452.

4: Cerutti G, Guo Y, Wang P, Nair MS, Wang M, Huang Y, Yu J, Liu L, Katsamba PS,
Bahna F, Reddem ER,
Kwong PD, Ho DD, Sheng Z, Shapiro L. Neutralizing antibody
5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal
domain
. Cell Rep. 2021 Oct 16:109928. doi: 10.1016/j.celrep.2021.109928. Epub
ahead of print. PMID: 34706271; PMCID: PMC8519878.

5: Fu J, Li Q, Liu X, Tu T, Lv X, Yin X, Lv J, Song Z, Qu J,
Zhang J, Li J, Gu
F. Human cell based directed evolution of adenine base editors with improved
efficiency
. Nat Commun. 2021 Oct 8;12(1):5897. doi: 10.1038/s41467-021-26211-0.
PMID: 34625552; PMCID: PMC8501064.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS Suggested Tips and/or Tricks?

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.

DISCUSSIONSSuggested Topics?

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, "Looking ahead to the next 50 years of the Protein Data Bank" (2021)

J.H. Chill and G.M. Clore, Biophysical methods: "Seeing is believing" (2021)

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 - virusMED , a powerful new resource to speed the development of vaccines and treatments to battle the next pandemic (Link)

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


Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


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

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