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Newsletter No. 451
September 20, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


AUGUST 2021 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Watkins JC, Evans RH, Bayés À, Booker SA, Gibb A, Mabb AM, Mayer M, Mellor
JR, Molnár E, Niu L, Ortega A, Pankratov Y, Ramos-Vicente D, Rodríguez-Campuzano
A, Rodríguez-Moreno A, Wang LY, Wang YT, Wollmuth L, Wyllie DJA, Zhuo M,
Frenguelli BG. 21st century excitatory amino acid research: A Q & A with Jeff
Watkins and Dick Evans. Neuropharmacology
. 2021 Aug 5;198:108743. doi:
10.1016/j.neuropharm.2021.108743. Epub ahead of print. PMID: 34363811.

2: Okuno Y, Yoo J, Schwieters CD, Best RB, Chung HS, Clore GM. Atomic view of
cosolute-induced protein denaturation probed by NMR solvent paramagnetic
relaxation enhancement
. Proc Natl Acad Sci U S A. 2021 Aug
24;118(34):e2112021118. doi: 10.1073/pnas.2112021118. PMID: 34404723.

3: Kosek D, Grabundzija I, Lei H, Bilic I, Wang H, Jin Y, Peaslee GF, Hickman
AB, Dyda F. The large bat Helitron DNA transposase forms a compact monomeric
assembly that buries and protects its covalently bound 5'-transposon end
. Mol
Cell. 2021 Aug 10:S1097-2765(21)00597-9. doi: 10.1016/j.molcel.2021.07.028. Epub
ahead of print. PMID: 34403695.

4: Parker JL, Deme JC, Wu Z, Kuteyi G, Huo J, Owens RJ, Biggin PC, Lea SM,
Newstead S. Cryo-EM structure of PepT2 reveals structural basis for proton-
coupled peptide and prodrug transport in mammals
. Sci Adv. 2021 Aug
25;7(35):eabh3355. doi: 10.1126/sciadv.abh3355. PMID: 34433568; PMCID:
PMC8386928.

5: 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 Aug
17:gkab719. doi: 10.1093/nar/gkab719. Epub ahead of print. PMID: 34403466;
PMCID: PMC8385992.

6: Bou-Nader C, Muecksch F, Brown JB, Gordon JM, York A, Peng C, Ghirlando R,
Summers MF, Bieniasz PD, Zhang J. HIV-1 matrix-tRNA complex structure reveals
basis for host control of Gag localization
. Cell Host Microbe. 2021 Aug
5:S1931-3128(21)00339-5. doi: 10.1016/j.chom.2021.07.006. Epub ahead of print.
PMID: 34384537.

7: Li M, Srp J, Mareš M, Wlodawer A, Gustchina A. Structural studies of
complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type
inhibitor BbKI
. Acta Crystallogr D Struct Biol. 2021 Aug 1;77(Pt 8):1084-1098.
doi: 10.1107/S2059798321006483. Epub 2021 Jul 29. PMID: 34342281; PMCID:
PMC8329858.

8: Frank I, Cigoli M, Arif MS, Fahlberg MD, Maldonado S, Calenda G, Pegu A, Yang
ES, Rawi R, Chuang GY, Geng H, Liu C, Zhou T,
Kwong PD, Arthos J, Cicala C,
Grasperge BF, Blanchard JL, Gettie A, Fennessey CM, Keele BF, Vaccari M, Hope
TJ, Fauci AS, Mascola JR, Martinelli E. Blocking α<sub>4</sub>β<sub>7</sub>
integrin delays viral rebound in SHIV<sub>SF162P3</sub>-infected macaques
treated with anti-HIV broadly neutralizing antibodies
. Sci Transl Med. 2021 Aug
18;13(607):eabf7201. doi: 10.1126/scitranslmed.abf7201. PMID: 34408080.

9: Olia AS, Tsybovsky Y, Chen SJ, Liu C, Nazzari AF, Ou L, Wang L, Kong WP,
Leung K, Liu T, Stephens T, Teng IT, Wang S, Yang ES, Zhang B, Zhang Y, Zhou T,
Mascola JR,
Kwong PD. SARS-CoV-2 S2P spike ages through distinct states with
altered immunogenicity
. J Biol Chem. 2021 Aug 27:101127. doi:
10.1016/j.jbc.2021.101127. Epub ahead of print. PMID: 34461095; PMCID:
PMC8393506.

10: Zhang J. The long and short of it: long noncoding RNAs in neural development
and diseases
. Front Biosci (Landmark Ed). 2021 Aug 30;26(8):258-261. doi:
10.52586/4941. PMID: 34455757.


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,


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


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

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