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Newsletter No. 430
October 5, 2020

ACA News, IUCr Newsletter, IUCr Meetings List


SEPTEMBER 2020 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Cheung CS, Fruehwirth A, Paparoditis PCG, Shen CH, Foglierini M, Joyce MG,
Leung K, Piccoli L, Rawi R, Silacci-Fregni C, Tsybovsky Y, Verardi R, Wang L,
Wang S, Yang ES, Zhang B, Zhang Y, Chuang GY, Corti D, Mascola JR, Shapiro L,
Kwong PD, Lanzavecchia A, Zhou T. Identification and Structure of a Multidonor
Class of Head-Directed Influenza-Neutralizing Antibodies Reveal the Mechanism
for Its Recurrent Elicitation
. Cell Rep. 2020 Sep 1;32(9):108088. doi:
10.1016/j.celrep.2020.108088. PMID: 32877670.

2: McCann KL, Kavari SL, Burkholder AB, Phillips BT, Hall TMT. H/ACA snoRNA
levels are regulated during stem cell differentiation
. Nucleic Acids Res. 2020
Sep 4;48(15):8686-8703. doi: 10.1093/nar/gkaa612. PMID: 32710630; PMCID:
PMC7470967.

3: Schmidt T, Clore GM. <i>T</i><sub>m</sub> filtering by <sup>1</sup>H-methyl
labeling in a deuterated protein for pulsed double electron-electron resonance
EPR
. Chem Commun (Camb). 2020 Sep 17;56(74):10890-10893. doi:
10.1039/d0cc04369a. PMID: 32940289; PMCID: PMC7498720.

4: Hua B, Jones CP, Mitra J, Murray PJ, Rosenthal R,
Ferré-D'Amaré AR, Ha T.
Real-time monitoring of single ZTP riboswitches reveals a complex and
kinetically controlled decision landscape
. Nat Commun. 2020 Sep 10;11(1):4531.
doi: 10.1038/s41467-020-18283-1. PMID: 32913225; PMCID: PMC7484762.

5: Brzezinski D, Kowiel M, Cooper DR, Cymborowski M, Grabowski M, Wlodawer A,
Dauter Z, Shabalin IG, Gilski M, Rupp B, Jaskolski M, Minor W.
Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related
structural models
. Protein Sci. 2020 Sep 27. doi: 10.1002/pro.3959. Epub ahead
of print. PMID: 32981130.

6: Xia D. Structural Snapshots of the Cellular Folded Protein Translocation
Machinery Bcs1
. FEBS J. 2020 Sep 26. doi: 10.1111/febs.15576. Epub ahead of
print. PMID: 32979284.

7: Soubias O, Pant S, Heinrich F, Zhang Y, Roy NS, Li J, Jian X, Yohe ME,
Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA. Membrane surface recognition by
the ASAP1 PH domain and consequences for interactions with the small GTPase
Arf1
. Sci Adv. 2020 Sep 30;6(40):eabd1882. doi: 10.1126/sciadv.abd1882. PMID:
32998886.

8: Bai Y, Zhou BR. Structures of Native-like Nucleosomes: One Step Closer toward
Understanding the Structure and Function of Chromatin
. J Mol Biol. 2020 Sep
11:S0022-2836(20)30539-8. doi: 10.1016/j.jmb.2020.09.007. Epub ahead of print.
PMID: 32920051.

9: Hu H,
Negishi M. RORα phosphorylation by casein kinase 1α as glucose signal
to regulate estrogen sulfation in human liver cells
. Biochem J. 2020 Sep
30;477(18):3583-3598. doi: 10.1042/BCJ20200427. PMID: 32686824.

10: Ruszkowska A, Ruszkowski M, Hulewicz JP,
Dauter Z, Brown JA. Molecular
structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples
.
Nucleic Acids Res. 2020 Sep 25:gkaa770. doi: 10.1093/nar/gkaa770. Epub ahead of
print. PMID: 32976568.

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)