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Newsletter No. 431
November 2, 2020

ACA News, IUCr Newsletter, IUCr Meetings List


OCTOBER 2020 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Corbett KS, Flynn B, Foulds KE, Francica JR, Boyoglu-Barnum S, Werner AP,
Flach B, O'Connell S, Bock KW, Minai M, Nagata BM, Andersen H, Martinez DR, Noe
AT, Douek N, Donaldson MM, Nji NN, Alvarado GS, Edwards DK, Flebbe DR, Lamb E,
Doria-Rose NA, Lin BC, Louder MK, O'Dell S, Schmidt SD, Phung E, Chang LA, Yap
C, Todd JM, Pessaint L, Van Ry A, Browne S, Greenhouse J, Putman-Taylor T,
Strasbaugh A, Campbell TA, Cook A, Dodson A, Steingrebe K, Shi W, Zhang Y,
Abiona OM, Wang L, Pegu A, Yang ES, Leung K, Zhou T, Teng IT, Widge A, Gordon I,
Novik L, Gillespie RA, Loomis RJ, Moliva JI, Stewart-Jones G, Himansu S, Kong
WP, Nason MC, Morabito KM, Ruckwardt TJ, Ledgerwood JE, Gaudinski MR,
Kwong PD,
Mascola JR, Carfi A, Lewis MG, Baric RS, McDermott A, Moore IN, Sullivan NJ,
Roederer M, Seder RA, Graham BS. Evaluation of the mRNA-1273 Vaccine against
SARS-CoV-2 in Nonhuman Primates
. N Engl J Med. 2020 Oct 15;383(16):1544-1555.
doi: 10.1056/NEJMoa2024671. Epub 2020 Jul 28. PMID: 32722908; PMCID: PMC7449230.

2: Strzelczyk P, Zhang D, Dyba M,
Wlodawer A, Lubkowski J. Generalized enzymatic
mechanism of catalysis by tetrameric L-asparaginases from mesophilic bacteria
.
Sci Rep. 2020 Oct 15;10(1):17516. doi: 10.1038/s41598-020-74480-4. PMID:
33060684; PMCID: PMC7567106.

3: Maiti A, Myint W, Delviks-Frankenberry KA, Hou S, Kanai T, Balachandran V,
Sierra Rodriguez C, Tripathi R, Kurt Yilmaz N, Pathak VK, Schiffer CA, Matsuo H.
Crystal structure of a soluble APOBEC3G variant suggests ssDNA to bind in a
channel that extends between the two domains
. J Mol Biol. 2020 Oct
21:S0022-2836(20)30597-0. doi: 10.1016/j.jmb.2020.10.020. Epub ahead of print.
PMID: 33098858.

4: Zhang B, Chao CW, Tsybovsky Y, Abiona OM, Hutchinson GB, Moliva JI, Olia AS,
Pegu A, Phung E, Stewart-Jones GBE, Verardi R, Wang L, Wang S, Werner A, Yang
ES, Yap C, Zhou T, Mascola JR, Sullivan NJ, Graham BS, Corbett KS,
Kwong PD. A
platform incorporating trimeric antigens into self-assembling nanoparticles
reveals SARS-CoV-2-spike nanoparticles to elicit substantially higher
neutralizing responses than spike alone
. Sci Rep. 2020 Oct 23;10(1):18149. doi:
10.1038/s41598-020-74949-2. PMID: 33097791; PMCID: PMC7584627.

5: Zhou T, Teng IT, Olia AS, Cerutti G, Gorman J, Nazzari A, Shi W, Tsybovsky Y,
Wang L, Wang S, Zhang B, Zhang Y, Katsamba PS, Petrova Y, Banach BB, Fahad AS,
Liu L, Lopez Acevedo SN, Madan B, Oliveira de Souza M, Pan X, Wang P, Wolfe JR,
Yin M, Ho DD, Phung E, DiPiazza A, Chang LA, Abiona OM, Corbett KS, DeKosky BJ,
Graham BS, Mascola JR, Misasi J, Ruckwardt T, Sullivan NJ, Shapiro L,
Kwong PD.
Structure-Based Design with Tag-Based Purification and In-Process Biotinylation
Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes
. Cell Rep.
2020 Oct 27;33(4):108322. doi: 10.1016/j.celrep.2020.108322. Epub 2020 Oct 12.
PMID: 33091382; PMCID: PMC7550166.

6: Kosek D, Hickman AB, Ghirlando R, He S, Dyda F. Structures of ISCth4
transpososomes reveal the role of asymmetry in copy-out/paste-in DNA
transposition
. EMBO J. 2020 Oct 2:e105666. doi: 10.15252/embj.2020105666. Epub
ahead of print. PMID: 33006208.

7: Bozóki B, Mótyán JA, Hoffka G, Waugh DS, Tőzsér J. Specificity Studies of the
Venezuelan Equine Encephalitis Virus Non-Structural Protein 2 Protease Using
Recombinant Fluorescent Substrates
. Int J Mol Sci. 2020 Oct 16;21(20):7686. doi:
10.3390/ijms21207686. PMID: 33081394; PMCID: PMC7593941.

8: Guerin J, Botos I, Zhang Z, Lundquist K, Gumbart JC, Buchanan SK. Structural
insight into toxin secretion by contact dependent growth inhibition
transporters
. Elife. 2020 Oct 22;9:e58100. doi: 10.7554/eLife.58100. Epub ahead
of print. PMID: 33089781.

9: Lu J, Sun PD. High affinity binding of SARS-CoV-2 spike protein enhances ACE2
carboxypeptidase activity
. J Biol Chem. 2020 Oct 29:jbc.RA120.015303. doi:
10.1074/jbc.RA120.015303. Epub ahead of print. PMID: 33122196.

10: He LH, Wang H, Liu Y, Kang M, Li T, Li CC, Tong AP, Zhu YB, Song YJ,
Savarino SJ, Prouty MG,
Xia D, Bao R. Chaperone-tip adhesin complex is vital for
synergistic activation of CFA/I fimbriae biogenesis
. PLoS Pathog. 2020 Oct
2;16(10):e1008848. doi: 10.1371/journal.ppat.1008848. PMID: 33007034; PMCID:
PMC7531860.

11: Frazier MN, Pillon MC, Kocaman S, Gordon J, Stanley RE. Structural overview
of macromolecular machines involved in ribosome biogenesis
. Curr Opin Struct
Biol. 2020 Oct 21;67:51-60. doi: 10.1016/j.sbi.2020.09.003. Epub ahead of print.
PMID: 33099228.

12: Tugarinov V, Karamanos TK,
Clore GM. Optimized selection of slow-relaxing
<sup>13</sup>C transitions in methyl groups of proteins: application to
relaxation dispersion
. J Biomol NMR. 2020 Oct 1. doi:
10.1007/s10858-020-00349-3. Epub ahead of print. PMID: 33006092.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS - New approach for  structure determination from tiny crystals

Many crystals can't be grown into crystals large enough for their atomic arrangements to be deciphered. To tackle this challenge, scientists at the U.S. DOE's Brookhaven National Laboratory and colleagues at Columbia University have developed a new approach for solving protein structure from tiny crystal. For details, please click the link.

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Biophysical Methods, Sample Preparation.

DISCUSSIONSTopic Suggestions?

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 - Recommendations?


DR. ZBIGNIEW DAUTER'S LECTURES AT THE NIH (2005)
 

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

           "Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage 

            with possible use of it for phasing"


LOW RESOLUTION PHASING AND REFINEMENT (2011)

 Data Collection Strategies (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

CRYSTAL CLEAR (2014)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 Understanding Biology Through Structure (2017)

 On the state of crystallography at the dawn of the electron microscopy revolution (2017)

 The Fascinating World of Crystallography (2018)

 Data science skills for referees: I biological X-ray crystallography  (2018)

Correcting the public record of biological crystallography (2019)

A Little Dictionary of Crystallography (2019)

Early history of cryo-cooling for macromolecular crystallography (2019)

Methods Comparison: XFEL vs microED (2020)

The data universe of structural biology (2020)

MicroED Methodology & Development (2020)

How to Speak, Lecture by Patrick Winston (2020)


 LINKS - PDB SARS-CoV-2 Resources (Link)

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
on the NIH-NCI-CCR-MCL server (https://mcl1.ncifcrf.gov)