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Newsletter No. 426
August 3, 2020

ACA News, IUCr Newsletter, IUCr Meetings List


JULY 2020 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Olivieri M, Cho T, Álvarez-Quilón A, Li K, Schellenberg MJ, Zimmermann M,
Hustedt N, Rossi SE, Adam S, Melo H, Heijink AM, Sastre-Moreno G, Moatti N,
Szilard RK, McEwan A, Ling AK, Serrano-Benitez A, Ubhi T, Feng S, Pawling J,
Delgado-Sainz I, Ferguson MW, Dennis JW, Brown GW, Cortés-Ledesma F,
Williams RS, Martin A, Xu D, Durocher D. A Genetic Map of the Response to DNA
Damage in Human Cells
. Cell. 2020 Jul 23;182(2):481-496.e21. doi:
10.1016/j.cell.2020.05.040. Epub 2020 Jul 9. PMID: 32649862; PMCID: PMC7384976.

2: 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 Jul 28. doi:
10.1056/NEJMoa2024671. Epub ahead of print. PMID: 32722908.

3:
Zhang J. Unboxing the T-box riboswitches-A glimpse into multivalent and
multimodal RNA-RNA interactions
. Wiley Interdiscip Rev RNA. 2020 Jul 6:e1600.
doi: 10.1002/wrna.1600. Epub ahead of print. PMID: 32633085.

4: Smietanska J, Sliwiak J, Gilski M, Dauter Z, Strzalka R, Wolny J, Jaskolski M.
A new modulated crystal structure of the ANS complex of the St John's wort
Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell
.
Acta Crystallogr D Struct Biol. 2020 Jul 1;76(Pt 7):653-667. doi:
10.1107/S2059798320006841. Epub 2020 Jun 17. PMID: 32627738; PMCID: PMC7336385.

5: McCann KL, Kavari SL, Burkholder AB, Phillips BT, Hall TMT. H/ACA snoRNA
levels are regulated during stem cell differentiation
. Nucleic Acids Res. 2020
Jul 25:gkaa612. doi: 10.1093/nar/gkaa612. Epub ahead of print. PMID: 32710630.

6: Singh K, Burkhardt M, Nakuchima S, Herrera R, Muratova O, Gittis AG,
Kelnhofer E, Reiter K, Smelkinson M, Veltri D, Swihart BJ, Shimp R Jr, Nguyen V,
Zhang B, MacDonald NJ, Duffy PE,
Garboczi DN, Narum DL. Structure and function
of a malaria transmission blocking vaccine targeting Pfs230 and Pfs230-Pfs48/45
proteins
. Commun Biol. 2020 Jul 24;3(1):395. doi: 10.1038/s42003-020-01123-9.
PMID: 32709983; PMCID: PMC7381611.

7: 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 Jul 28:gkaa627. doi: 10.1093/nar/gkaa627. Epub ahead of print. PMID:
32719843.

8: Shindo S, Chen SH, Gotoh S, Yokobori K, Hu H, Ray M, Moore R, Nagata K,
Martinez J, Hong JS, Negishi M. Estrogen receptor α phosphorylated at Ser216
confers inflammatory function to mouse microglia
. Cell Commun Signal. 2020 Jul
29;18(1):117. doi: 10.1186/s12964-020-00578-x. PMID: 32727504.

9: Liu L, Wang P, Nair MS, Yu J, Rapp M, Wang Q, Luo Y, Chan JF, Sahi V,
Figueroa A, Guo XV, Cerutti G, Bimela J, Gorman J, Zhou T, Chen Z, Yuen KY,
Kwong PD, Sodroski JG, Yin MT, Sheng Z, Huang Y, Shapiro L, Ho DD. Potent
neutralizing antibodies directed to multiple epitopes on SARS-CoV-2 spike
.
Nature. 2020 Jul 22. doi: 10.1038/s41586-020-2571-7. Epub ahead of print. PMID:
32698192.

10: Diederichs KA, Ni X, Rollauer SE, Botos I, Tan X, King MS, Kunji ERS, Jiang
J, Buchanan SK. Structural insight into mitochondrial β-barrel outer membrane
protein biogenesis
. Nat Commun. 2020 Jul 3;11(1):3290. doi:
10.1038/s41467-020-17144-1. PMID: 32620929; PMCID: PMC7335169.

11: Chen Q, Luo W, Veach RA, Hickman AB, Wilson MH,
Dyda F. Structural basis of
seamless excision and specific targeting by piggyBac transposase
. Nat Commun.
2020 Jul 10;11(1):3446. doi: 10.1038/s41467-020-17128-1. PMID: 32651359; PMCID:
PMC7351741.

12: Osei-Amponsa V, Sridharan V, Tandon M, Evans CN, Klarmann K, Cheng KT, Lack
J, Chari R, Walters KJ. Impact of losing hRpn13 Pru or UCHL5 on proteasome
clearance of ubiquitinated proteins and RA190 cytotoxicity
. Mol Cell Biol. 2020
Jul 6:MCB.00122-20. doi: 10.1128/MCB.00122-20. Epub ahead of print. PMID:
32631902.

13: Ceccon A, Tugarinov V,
Clore GM. Kinetics of Fast Tetramerization of the
Huntingtin Exon 1 Protein Probed by Concentration-Dependent On-Resonance
<i>R</i><sub>1ρ</sub> Measurements
. J Phys Chem Lett. 2020 Jul
16;11(14):5643-5648. doi: 10.1021/acs.jpclett.0c01636. Epub 2020 Jul 1. PMID:
32589032; PMCID: PMC7377354.

14: Batra VK, Wilson SH. Structure of a DNA polymerase abortive complex with the
8OG:dA base pair at the primer terminus
. Commun Biol. 2020 Jul 3;3(1):348. doi:
10.1038/s42003-020-1080-4. PMID: 32620932; PMCID: PMC7334213.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - New approach for solving protein structures                                                           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.

TOPIC DISCUSSIONSuggestions?

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 - MicroED methodology & development (Link)


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)

 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)