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Newsletter No. 433
December 7, 2020

ACA News, IUCr Newsletter, IUCr Meetings List


NOVEMBER 2020 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Ratliff AC,
Buchanan SK, Celia H. Ton motor complexes. Curr Opin Struct Biol.
2020 Nov 3;67:95-100. doi: 10.1016/j.sbi.2020.09.014. Epub ahead of print. PMID:
33157479.

2: Celia H, Botos I, Ni X, Fox T, de Val N, Lloubes R, Jiang J,
Buchanan SK.
Author Correction: Cryo-EM structure of the bacterial Ton motor subcomplex ExbB-
ExbD provides information on structure and stoichiometry
. Commun Biol. 2020 Nov
9;3(1):676. doi: 10.1038/s42003-020-01427-w. Erratum for: Commun Biol. 2019 Oct
4;2:358. PMID: 33168926; PMCID: PMC7652868.

3:
Kwong PD, DeKosky BJ, Ulmer JB. Antibody-guided structure-based vaccines.
Semin Immunol. 2020 Nov 24:101428. doi: 10.1016/j.smim.2020.101428. Epub ahead
of print. PMID: 33246736.

4: O'Carroll IP, Fan L, Kroupa T, McShane EK, Theodore C, Yates EA, Kondrup B,
Ding J, Martin TS, Rein A, Wang YX. Structural Mimicry Drives HIV-1 Rev-Mediated
HERV-K Expression
. J Mol Biol. 2020 Nov 14;432(24):166711. doi:
10.1016/j.jmb.2020.11.010. Epub ahead of print. PMID: 33197463.

5: Chen X, Htet ZM, López-Alfonzo E, Martin A, Walters KJ. Proteasome
interaction with ubiquitinated substrates: from mechanisms to therapies
. FEBS J.
2020 Nov 19. doi: 10.1111/febs.15638. Epub ahead of print. PMID: 33211406.

6: Beyer HM, Virtanen SI, Aranko AS, Mikula KM, Lountos GT,
Wlodawer A, Ollila
OHS, Iwaï H. The Convergence of the Hedgehog/Intein Fold in Different Protein
Splicing Mechanisms
. Int J Mol Sci. 2020 Nov 7;21(21):8367. doi:
10.3390/ijms21218367. PMID: 33171880; PMCID: PMC7664689.

7: Kotov V, Mlynek G, Vesper O, Pletzer M, Wald J, Teixeira-Duarte CM, Celia H,
Garcia-Alai M, Nussberger S,
Buchanan SK, Morais-Cabral JH, Loew C, Djinovic-
Carugo K, Marlovits TC. In-depth interrogation of protein thermal unfolding data
with MoltenProt
. Protein Sci. 2020 Nov 2. doi: 10.1002/pro.3986. Epub ahead of
print. PMID: 33140490.

8: Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR,
Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human
Linker Histone Isoforms
. Mol Cell. 2020 Nov 16:S1097-2765(20)30772-3. doi:
10.1016/j.molcel.2020.10.038. Epub ahead of print. PMID: 33238161.

9: Rawi R, Rutten L, Lai YT, Olia AS, Blokland S, Juraszek J, Shen CH, Tsybovsky
Y, Verardi R, Yang Y, Zhang B, Zhou T, Chuang GY,
Kwong PD, Langedijk JPM.
Automated Design by Structure-Based Stabilization and Consensus Repair to
Achieve Prefusion-Closed Envelope Trimers in a Wide Variety of HIV Strains
. Cell
Rep. 2020 Nov 24;33(8):108432. doi: 10.1016/j.celrep.2020.108432. PMID:
33238130; PMCID: PMC7714614.

10: Karamanos TK, Tugarinov V,
Clore GM. An S/T motif controls reversible
oligomerization of the Hsp40 chaperone DNAJB6b through subtle reorganization of
a β sheet backbone
. Proc Natl Acad Sci U S A. 2020 Dec 1;117(48):30441-30450.
doi: 10.1073/pnas.2020306117. Epub 2020 Nov 16. PMID: 33199640.

11: Lee KS, Park JE, Ahn JI, Zeng Y. Constructing PCM with architecturally
distinct higher-order assemblies
. Curr Opin Struct Biol. 2020 Nov 8;66:66-73.
doi: 10.1016/j.sbi.2020.09.013. Epub ahead of print. PMID: 33176265.

12: Wu W, Cheng N, Black LW, Dietz H, Steven AC. Biphasic Packing of DNA and
Internal Proteins in Bacteriophage T4 Heads Revealed by Bubblegram Imaging
.
Viruses. 2020 Nov 10;12(11):1282. doi: 10.3390/v12111282. PMID: 33182609; PMCID:
PMC7697877.

13: Lu M, Uchil PD, Li W, Zheng D, Terry DS, Gorman J, Shi W, Zhang B, Zhou T,
Ding S, Gasser R, Prévost J, Beaudoin-Bussières G, Anand SP, Laumaea A, Grover
JR, Liu L, Ho DD, Mascola JR, Finzi A,
Kwong PD, Blanchard SC, Mothes W. Real-
Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles
. Cell Host
Microbe. 2020 Nov 13:S1931-3128(20)30618-1. doi: 10.1016/j.chom.2020.11.001.
Epub ahead of print. PMID: 33242391; PMCID: PMC7664471.

14: 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 Nov
4;48(19):10953-10972. doi: 10.1093/nar/gkaa784. PMID: 33045735; PMCID:
PMC7641761.

15: Alverez CN, Park JE, Toti KS, Xia Y, Krausz KW, Rai G, Bang JK, Gonzalez FJ,
Jacobson KA,
Lee KS. Identification of a New Heterocyclic Scaffold for
Inhibitors of the Polo-Box Domain of Polo-like Kinase 1
. J Med Chem. 2020 Nov
25;63(22):14087-14117. doi: 10.1021/acs.jmedchem.0c01669. Epub 2020 Nov 11.
PMID: 33175530.

16: Gunasekaran P, Yim MS, Ahn M, Soung NK, Park JE, Kim J, Bang G, Shin SC,
Choi J, Kim M, Kim HN, Lee YH, Chung YH, Lee K, EunKyeong Kim E, Jeon YH, Kim
MJ, Lee KR, Kim BY,
Lee KS, Ryu EK, Bang JK. Development of a Polo-like Kinase-1
Polo-Box Domain Inhibitor as a Tumor Growth Suppressor in Mice Models
. J Med
Chem. 2020 Nov 3. doi: 10.1021/acs.jmedchem.0c01451. Epub ahead of print. PMID:
33142063.

17: Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS,
Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry
M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD,
Mascola JR, Shapiro L,
Kwong PD. Cryo-EM Structures of SARS-CoV-2 Spike without
and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of
Receptor-Binding Domains
. Cell Host Microbe. 2020 Nov 17:S1931-3128(20)30621-1.
doi: 10.1016/j.chom.2020.11.004. Epub ahead of print. PMID: 33271067; PMCID:
PMC7670890.

18: Roark RS, Li H, Williams WB, Chug H, Mason RD, Gorman J, Wang S, Lee FH,
Rando J, Bonsignori M, Hwang KK, Saunders KO, Wiehe K, Moody MA, Hraber PT, Wagh
K, Giorgi EE, Russell RM, Bibollet-Ruche F, Liu W, Connell J, Smith AG, DeVoto
J, Murphy AI, Smith J, Ding W, Zhao C, Chohan N, Okumura M, Rosario C, Ding Y,
Lindemuth E, Bauer AM, Bar KJ, Ambrozak D, Chao CW, Chuang GY, Geng H, Lin BC,
Louder MK, Nguyen R, Zhang B, Lewis MG, Raymond D, Doria-Rose NA, Schramm CA,
Douek DC, Roederer M, Kepler TB, Kelsoe G, Mascola JR,
Kwong PD, Korber BT,
Harrison SC, Haynes BF, Hahn BH, Shaw GM. Recapitulation of HIV-1 Env-antibody
coevolution in macaques leading to neutralization breadth
. Science. 2020 Nov
19:eabd2638. doi: 10.1126/science.abd2638. Epub ahead of print. PMID: 33214287.

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.

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)