logo3

Newsletter No. 419
April 20, 2020

ACA News, IUCr Newsletter, IUCr Meetings List


MARCH 2020 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Nadalutti CA, Stefanick DF, Zhao ML, Horton JK, Prasad R, Brooks AM, Griffith 
JD,
Wilson SH. Mitochondrial dysfunction and DNA damage accompany enhanced levels
of formaldehyde in cultured primary human fibroblasts
. Sci Rep. 2020 Mar
27;10(1):5575. doi: 10.1038/s41598-020-61477-2. PubMed PMID: 32221313; PubMed
Central PMCID: PMC7101401.

2: Byrd RA. Could confounding the allosteric communication of biotic machinery be
an alternative path to antibiotics
? Proc Natl Acad Sci U S A. 2020 Mar 20. pii:
202002666. doi: 10.1073/pnas.2002666117. [Epub ahead of print] PubMed PMID:
32198204.

3: 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 Failur
e. J Viral Hepat. 2020
Mar 20. doi: 10.1111/jvh.13290. [Epub ahead of print] PubMed PMID: 32196859.

4: Yi M, Fashe M, Arakawa S, Moore R, Sueyoshi T, Negishi M. Nuclear receptor
CAR-ERα signaling regulates the estrogen sulfotransferase gene in the liver
. Sci
Rep. 2020 Mar 19;10(1):5001. doi: 10.1038/s41598-020-61767-9. PubMed PMID:
32193417; PubMed Central PMCID: PMC7081254.

5: Lu X, Ebelle DL, Matsuo H,
Walters KJ. An Extended Conformation for K48
Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure
.
Structure. 2020 Mar 9. pii: S0969-2126(20)30071-X. doi:
10.1016/j.str.2020.02.007. [Epub ahead of print] PubMed PMID: 32160516.

6: Buel GR, Chen X, Chari R, O'Neill MJ, Ebelle DL, Jenkins C, Sridharan V,
Tarasov SG, Tarasova NI, Andresson T, Walters KJ. Structure of E3 ligase E6AP
with a proteasome-binding site provided by substrate receptor hRpn10
. Nat Commun.
2020 Mar 10;11(1):1291. doi: 10.1038/s41467-020-15073-7. PubMed PMID: 32157086;
PubMed Central PMCID: PMC7064531.

7: Shen CH, DeKosky BJ, Guo Y, Xu K, Gu Y, Kilam D, Ko SH, Kong R, Liu K, Louder
MK, Ou L, Zhang B, Chao CW, Corcoran MM, Feng E, Huang J, Normandin E, O'Dell S,
Ransier A, Rawi R, Sastry M, Schmidt SD, Wang S, Wang Y, Chuang GY, Doria-Rose
NA, Lin B, Zhou T, Boritz EA, Connors M, Douek DC, Karlsson Hedestam GB, Sheng Z,
Shapiro L, Mascola JR,
Kwong PD. VRC34-Antibody Lineage Development Reveals How a
Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage
.
Cell Host Microbe. 2020 Mar 3. pii: S1931-3128(20)30070-6. doi:
10.1016/j.chom.2020.01.027. [Epub ahead of print] PubMed PMID: 32130953.

8: Ceccon A, Tugarinov V, Ghirlando R, Clore GM. Abrogation of prenucleation,
transient oligomerization of the Huntingtin exon 1 protein by human profilin I
.
Proc Natl Acad Sci U S A. 2020 Mar 17;117(11):5844-5852. doi:
10.1073/pnas.1922264117. Epub 2020 Mar 3. PubMed PMID: 32127471; PubMed Central
PMCID: PMC7084121.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Contributions?

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 - XFEL vs microED (Link)


Methods Comparison: XFEL vs microED (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)

 LINKS SARS-CoV-2 Related Structures (Link)

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry
                  SARS-CoV-2 Related Structures,


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)