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Newsletter No. 435
January 4, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


DECEMBER 2020 PUBLICATIONS BY MEMBERS OF THE GROUP


1:
Thapar R, Wang JL, Hammel M, Ye R, Liang K, Sun C, Hnizda A, Liang S, Maw SS,
Lee L, Villarreal H, Forrester I, Fang S, Tsai MS, Blundell TL, Davis AJ, Lin C,
Lees-Miller SP, Strick TR, Tainer JA. Mechanism of efficient double-strand break
repair by a long non-coding RNA
. Nucleic Acids Res. 2020 Dec 18:gkaa1233. doi:
10.1093/nar/gkaa1233. Epub ahead of print. PMID: 33337499.

2: Khago D, Fucci IJ, Byrd RA. The Role of Conformational Dynamics in the
Recognition and Regulation of Ubiquitination
. Molecules. 2020 Dec
15;25(24):5933. doi: 10.3390/molecules25245933. PMID: 33333809; PMCID:
PMC7765195.

3: Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M,
Yang W. Structure of an activated DNA-PK and its implications for NHEJ. Mol
Cell. 2020 Dec 24:S1097-2765(20)30907-2. doi: 10.1016/j.molcel.2020.12.015. Epub
ahead of print. PMID: 33385326.

4: Teramoto T, Kaitany KJ, Kakuta Y, Kimura M, Fierke CA, Hall TMT.
Pentatricopeptide repeats of protein-only RNase P use a distinct mode to
recognize conserved bases and structural elements of pre-tRNA
. Nucleic Acids
Res. 2020 Dec 2;48(21):11815-11826. doi: 10.1093/nar/gkaa627. PMID: 32719843;
PMCID: PMC7708040.

5: Mogus AT, Liu L, Jia M, Ajayi DT, Xu K, Kong R, Huang J, Yu J,
Kwong PD,
Mascola JR, Ho DD, Tsuji M, Chackerian B. Virus-Like Particle Based Vaccines
Elicit Neutralizing Antibodies against the HIV-1 Fusion Peptide
. Vaccines
(Basel). 2020 Dec 15;8(4):765. doi: 10.3390/vaccines8040765. PMID: 33333740;
PMCID: PMC7765226.

6: Verardi R, Lindesmith LC, Tsybovsky Y, Gorman J, Chuang GY, Edwards CE,
Brewer-Jensen PD, Mallory ML, Ou L, Schön A, Shi W, Tully ES, Georgiou G, Baric
RS,
Kwong PD. Disulfide stabilization of human norovirus GI.1 virus-like
particles focuses immune response toward blockade epitopes
. NPJ Vaccines. 2020
Dec 14;5(1):110. doi: 10.1038/s41541-020-00260-w. PMID: 33318483; PMCID:
PMC7736355.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS - Reliable cryo-EM resolution estimation

A modified Fourier shell correlation (FSC) moehodology is introduced by Pawel Penczek, which is aimed addressing two fundamental problems that mar the use of FSC: the strong influence of mask-induced artifacts on resolution estimation and the lack of assessment of FSC uncertaninties stemming from the inability to determine the asscociated number of degrees of freedom. For details, please click the link.

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.

DISCUSSIONSWhat do you as a structural biologist think of the use of AI by DeepMind to predict protein folds?

Please find an analysis by Prof. John Helliwell and share your thoughts with the community.

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)