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Newsletter No. 428
September 7, 2020

ACA News, IUCr Newsletter, IUCr Meetings List


AUGUST 2020 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Zhou X, Peters HK 3rd, Li X, Costantino N, Kumari V, Shi G, Tu C, Cameron TA,
Haeusser DP, Vega DE, Ji X, Margolin W, Court DL. Overproduction of a dominant
mutant of the conserved Era GTPase inhibits cell division in <i>Escherichia
coli</i>
. J Bacteriol. 2020 Aug 17:JB.00342-20. doi: 10.1128/JB.00342-20. Epub
ahead of print. PMID: 32817092.

2: Heymann JB, Wang B, Newcomb WW, Wu W, Winkler DC, Cheng N, Reilly ER, Hsia
RC, Thomas JA, Steven AC. The Mottled Capsid of the <i>Salmonella</i> Giant
Phage SPN3US, a Likely Maturation Intermediate with a Novel Internal Shell.
Viruses
. 2020 Aug 19;12(9):E910. doi: 10.3390/v12090910. PMID: 32825132.

3: Hu H, Yokobori K,
Negishi M. PXR phosphorylated at Ser350 transduces a
glucose signal to repress the estrogen sulfotransferase gene in human liver
cells and fasting signal in mouse livers
. Biochem Pharmacol. 2020 Aug
14;180:114197. doi: 10.1016/j.bcp.2020.114197. Epub ahead of print. PMID:
32798464.

4: Chen Z, Engle RE, Shen CH, Zhao H, Schuck PW, Danoff EJ, Nguyen H, Nishimura
N, Bock KW, Moore IN,
Kwong PD, Purcell RH, Govindarajan S, Farci P. Distinct
disease features in chimpanzees infected with a precore HBV mutant associated
with acute liver failure in humans
. PLoS Pathog. 2020 Aug 31;16(8):e1008793.
doi: 10.1371/journal.ppat.1008793. Epub ahead of print. PMID: 32866189.

5: Choi WS, He P, Pothukuchy A, Gollihar J, Ellington AD, Yang W. How a B family
DNA polymerase has been evolved to copy RNA
. Proc Natl Acad Sci U S A. 2020 Aug
17:202009415. doi: 10.1073/pnas.2009415117. Epub ahead of print. PMID: 32817521.

6: Lee KS, Park JE, Il Ahn J, Wei Z, Zhang L. A self-assembled cylindrical
platform for Plk4-induced centriole biogenesis
. Open Biol. 2020
Aug;10(8):200102. doi: 10.1098/rsob.200102. Epub 2020 Aug 19. PMID: 32810424.

7: Chen Z, Shen CH, Engle RE, Zamboni F,
Kwong PD, Purcell RH, Farci P. Next-
generation sequencing of the intrahepatic antibody repertoire delineates a
unique B-cell response in HBV-associated acute liver failure
. J Viral Hepat.
2020 Aug;27(8):847-851. doi: 10.1111/jvh.13290. Epub 2020 Apr 3. PMID: 32196859.

8: Lakshmipathy DR, Cudrici CD,
Dyda F, Xu W, Ferrante EA, Nguyen DT, Carney KM,
Rollison S, Chen MY, Nesti LJ, Boehm M, Brofferio A, Wen H. Morphology and
chemical identity of periarticular and vascular calcification in a patient with
the rare genetic disease of arterial calcification due to deficiency of CD73
(ACDC)
. Radiol Case Rep. 2020 Aug 14;15(10):1883-1886. doi:
10.1016/j.radcr.2020.07.056. PMID: 32874378; PMCID: PMC7452020.

9: Liu Y, Rodriguez Y, Ross RL, Zhao R, Watts JA, Grunseich C, Bruzel A, Li D,
Burdick JT, Prasad R, Crouch RJ, Limbach PA,
Wilson SH, Cheung VG. RNA abasic
sites in yeast and human cells
. Proc Natl Acad Sci U S A. 2020 Aug
25;117(34):20689-20695. doi: 10.1073/pnas.2011511117. Epub 2020 Aug 11. PMID:
32788345.

10: Hayne CK, Schmidt CA, Haque MI, Matera AG, Stanley RE. Reconstitution of the
human tRNA splicing endonuclease complex: insight into the regulation of pre-
tRNA cleavage
. Nucleic Acids Res. 2020 Aug 20;48(14):7609-7622. doi:
10.1093/nar/gkaa438. PMID: 32476018.

11: Cheng C, Duan H, Xu K, Chuang GY, Corrigan AR, Geng H, O'Dell S, Ou L,
Chambers M, Changela A, Chen X, Foulds KE, Sarfo EK, Jafari AJ, Hill KR, Kong R,
Liu K, Todd JP, Tsybovsky Y, Verardi R, Wang S, Wang Y, Wu W, Zhou T; VRC
Production Program, Arnold FJ, Doria-Rose NA, Koup RA, McDermott AB, Scorpio DG,
Worobey M, Shapiro L, Mascola JR,
Kwong PD. Immune Monitoring Reveals Fusion
Peptide Priming to Imprint Cross-Clade HIV-Neutralizing Responses with a
Characteristic Early B Cell Signature
. Cell Rep. 2020 Aug 4;32(5):107981. doi:
10.1016/j.celrep.2020.107981. PMID: 32755575.

12: Chen X, Dorris Z, Shi D, Huang RK, Khant H, Fox T, de Val N, Williams D,
Zhang P,
Walters KJ. Cryo-EM Reveals Unanchored M1-Ubiquitin Chain Binding at
hRpn11 of the 26S Proteasome
. Structure. 2020 Aug 5:S0969-2126(20)30244-6. doi:
10.1016/j.str.2020.07.011. Epub ahead of print. PMID: 32783951.

13: Tran B, Pichling P, Tenney L, Connelly CM, Moon MH, Ferré-D'Amaré AR,
Schneekloth JS Jr, Jones CP. Parallel Discovery Strategies Provide a Basis for
Riboswitch Ligand Design
. Cell Chem Biol. 2020 Aug 10:S2451-9456(20)30294-4.
doi: 10.1016/j.chembiol.2020.07.021. Epub ahead of print. PMID: 32795418.

14: Majumder P, Zhang Y, Iglesias M, Fan L, Kelley JA, Andrews C, Patel N,
Stagno JR, Oh BC, Furtmüller GJ, Lai CC, Wang YX, Brandacher G, Raimondi G,
Schneider JP. Multiphase Assembly of Small Molecule Microcrystalline Peptide
Hydrogel Allows Immunomodulatory Combination Therapy for Long-Term Heart
Transplant Survival
. Small. 2020 Aug 18:e2002791. doi: 10.1002/smll.202002791.
Epub ahead of print. PMID: 32812339.

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 How to Speak by Patrick Winston  (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)

MicroED Methodology & Development (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)