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Newsletter No. 437
February 1, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


JANUARY 2021 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Maiti A, Hou S, Schiffer CA, Matsuo H. Interactions of APOBEC3s with DNA and
RNA
. Curr Opin Struct Biol. 2021 Jan 21;67:195-204. doi:
10.1016/j.sbi.2020.12.004. Epub ahead of print. PMID: 33486429.

2: Lee KS, Steinmetz MO. Centrosomes in the spotlight: from organization to
function to role in disease
. Curr Opin Struct Biol. 2021 Jan
20:S0959-440X(21)00001-4. doi: 10.1016/j.sbi.2021.01.001. Epub ahead of print.
PMID: 33485756.

3: Williams JS, Tumbale PP, Arana ME, Rana JA,
Williams RS, Kunkel TA. High-
fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA
replication
. Nat Commun. 2021 Jan 20;12(1):482. doi: 10.1038/s41467-020-20800-1.
PMID: 33473124; PMCID: PMC7817679.

4: Jurkiw TJ, Tumbale PP, Schellenberg MJ, Cunningham-Rundles C, Williams RS,
O'Brien PJ. LIG1 syndrome mutations remodel a cooperative network of ligand
binding interactions to compromise ligation efficiency
. Nucleic Acids Res. 2021
Jan 14:gkaa1297. doi: 10.1093/nar/gkaa1297. Epub ahead of print. PMID: 33444456.

5: Salinas E, Boisvert M, Upadhyay AA, Bédard N, Nelson SA, Bruneau J, Derdeyn
CA, Marcotrigiano J, Evans MJ, Bosinger SE, Shoukry NH, Grakoui A. Early T
follicular helper cell activity accelerates hepatitis C virus-specific B cell
expansion
. J Clin Invest. 2021 Jan 19;131(2):e140590. doi: 10.1172/JCI140590.
PMID: 33463551; PMCID: PMC7810471.

6: Jaskolski M,
Wlodawer A, Dauter Z, Shabalin I, Chruszcz M. Celebrating the
75th birthday of Professor Wladek Minor, one of the most accomplished Polish-
American structural biologists
. Acta Biochim Pol. 2021 Jan 21. doi:
10.18388/abp.2020_5539. Epub ahead of print. PMID: 33476109.

7: Chen X, Zhou T, Schmidt SD, Duan H, Cheng C, Chuang GY, Gu Y, Louder MK, Lin
BC, Shen CH, Sheng Z, Zheng MX, Doria-Rose NA, Joyce MG, Shapiro L, Tian M, Alt
FW,
Kwong PD, Mascola JR. Vaccination induces maturation in a mouse model of
diverse unmutated VRC01-class precursors to HIV-neutralizing antibodies with
>50% breadth
. Immunity. 2021 Jan 7:S1074-7613(20)30542-2. doi:
10.1016/j.immuni.2020.12.014. Epub ahead of print. PMID: 33453152.

8: Hattori SI, Higashi-Kuwata N, Hayashi H, Allu SR, Raghavaiah J, Bulut H, Das
D, Anson BJ, Lendy EK, Takamatsu Y, Takamune N, Kishimoto N, Murayama K,
Hasegawa K, Li M, Davis DA, Kodama EN, Yarchoan R, Wlodawer A, Misumi S, Mesecar
AD, Ghosh AK, Mitsuya H. A small molecule compound with an indole moiety
inhibits the main protease of SARS-CoV-2 and blocks virus replication
. Nat
Commun. 2021 Jan 28;12(1):668. doi: 10.1038/s41467-021-20900-6. PMID: 33510133.

9: Yang Y, Shi W, Abiona OM, Nazzari A, Olia AS, Ou L, Phung E, Stephens T,
Tsybovsky Y, Verardi R, Wang S, Werner A, Yap C, Ambrozak D, Bylund T, Liu T,
Nguyen R, Wang L, Zhang B, Zhou T, Chuang GY, Graham BS, Mascola JR, Corbett KS,
Kwong PD. Newcastle Disease Virus-Like Particles Displaying Prefusion-Stabilized
SARS-CoV-2 Spikes Elicit Potent Neutralizing Responses
. Vaccines (Basel). 2021
Jan 21;9(2):73. doi: 10.3390/vaccines9020073. PMID: 33494381.

10: Pillon MC, Frazier MN, Dillard LB, Williams JG, Kocaman S, Krahn JM, Perera
L, Hayne CK, Gordon J, Stewart ZD, Sobhany M, Deterding LJ, Hsu AL, Dandey VP,
Borgnia MJ, Stanley RE. Cryo-EM structures of the SARS-CoV-2 endoribonuclease
Nsp15 reveal insight into nuclease specificity and dynamics
. Nat Commun. 2021
Jan 27;12(1):636. doi: 10.1038/s41467-020-20608-z. PMID: 33504779; PMCID:
PMC7840905.

11: Chen X, Shi D, Zhang P, Walters KJ. An optimized protocol for acquiring and
processing cryo-EM data of human 26S proteasome with M1-Ub<sub>6</sub>
. STAR
Protoc. 2021 Jan 18;2(1):100278. doi: 10.1016/j.xpro.2020.100278. PMID:
33521680; PMCID: PMC7820132.

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 - Jennifer Doudna, Nobel Lecture 2020


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)