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Newsletter No. 425
July 20 2020

ACA News, IUCr Newsletter, IUCr Meetings List


JUNE 2020 PUBLICATIONS BY MEMBERS OF THE GROU

1: Stix R, Lee CJ, Faraldo-Gómez JD, Banerjee A. Structure and Mechanism of DHHC
Protein Acyltransferases
. J Mol Biol. 2020 Jun 6:S0022-2836(20)30372-7. doi:
10.1016/j.jmb.2020.05.023. Epub ahead of print. PMID: 32522557.

2: Saha LK, Wakasugi M, Akter S, Prasad R, Wilson SH, Shimizu N, Sasanuma H,
Huang SN, Agama K, Pommier Y, Matsunaga T, Hirota K, Iwai S, Nakazawa Y, Ogi T,
Takeda S. Topoisomerase I-driven repair of UV-induced damage in NER-deficient
cells
. Proc Natl Acad Sci U S A. 2020 Jun 23;117(25):14412-14420. doi:
10.1073/pnas.1920165117. Epub 2020 Jun 8. PMID: 32513688; PMCID: PMC7321995.

3: Bou-Nader C, Zhang J. Structural Insights into RNA Dimerization: Motifs,
Interfaces and Functions
. Molecules. 2020 Jun 23;25(12):E2881. doi:
10.3390/molecules25122881. PMID: 32585844.

4: Chuang GY, Lai YT, Boyington JC, Cheng C, Geng H, Narpala S, Rawi R, Schmidt
SD, Tsybovsky Y, Verardi R, Xu K, Yang Y, Zhang B, Chambers M, Changela A,
Corrigan AR, Kong R, Olia AS, Ou L, Sarfo EK, Wang S, Wu W, Doria-Rose NA,
McDermott AB, Mascola JR,
Kwong PD. Development of a 3Mut-Apex-Stabilized
Envelope Trimer That Expands HIV-1 Neutralization Breadth When Used To Boost
Fusion Peptide-Directed Vaccine-Elicited Responses
. J Virol. 2020 Jun
16;94(13):e00074-20. doi: 10.1128/JVI.00074-20. PMID: 32295908.

5: Jin W, Madan B, Mussman BK, Hailemariam AT, Fahad AS, Wolfe JR, Kwon YD,
Zhang B, Shapiro L,
Kwong PD, DeKosky BJ. The covalent SNAP tag for protein
display quantification and low-pH protein engineering
. J Biotechnol. 2020 Jun
16;320:50-56. doi: 10.1016/j.jbiotec.2020.06.011. Epub ahead of print. PMID:
32561362.

6: Schellenberg MJ, Appel CD, Riccio AA, Butler LR, Krahn JM, Liebermann JA,
Cortés-Ledesma F,
Williams RS. Ubiquitin stimulated reversal of topoisomerase 2
DNA-protein crosslinks by TDP2
. Nucleic Acids Res. 2020 Jun 19;48(11):6310-6325.
doi: 10.1093/nar/gkaa318. PMID: 32356875; PMCID: PMC7293035.

7: 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 Jun 1:gkaa438. doi: 10.1093/nar/gkaa438.
Epub ahead of print. PMID: 32476018.

8: Van Laethem F, Saba I, Lu J, Bhattacharya A, Tai X, Guinter TI, Engelhardt B,
Alag A, Rojano M, Ashe JM, Hanada KI, Yang JC,
Sun PD, Singer A. Novel MHC-
Independent αβTCRs Specific for CD48, CD102, and CD155 Self-Proteins and Their
Selection in the Thymus
. Front Immunol. 2020 Jun 16;11:1216. doi:
10.3389/fimmu.2020.01216. PMID: 32612609; PMCID: PMC7308553.

9: Guardia CM, Tan XF, Lian T, Rana MS, Zhou W, Christenson ET, Lowry AJ,
Faraldo-Gómez JD, Bonifacino JS, Jiang J,
Banerjee A. Structure of Human ATG9A,
the Only Transmembrane Protein of the Core Autophagy Machinery
. Cell Rep. 2020
Jun 30;31(13):107837. doi: 10.1016/j.celrep.2020.107837. PMID: 32610138.

10: Martin-Martin I, Paige A, Valenzuela Leon PC, Gittis AG, Kern O, Bonilla B,
Chagas AC, Ganesan S, Smith LB, Garboczi DN, Calvo E. ADP binding by the Culex
quinquefasciatus mosquito D7 salivary protein enhances blood feeding on mammals
.
Nat Commun. 2020 Jun 9;11(1):2911. doi: 10.1038/s41467-020-16665-z. PMID:
32518308; PMCID: PMC7283271.

11: Álvarez-Quilón A, Wojtaszek JL, Mathieu MC, Patel T, Appel CD, Hustedt N,
Rossi SE, Wallace BD, Setiaputra D, Adam S, Ohashi Y, Melo H, Cho T, Gervais C,
Muñoz IM, Grazzini E, Young JTF, Rouse J, Zinda M,
Williams RS, Durocher D.
Endogenous DNA 3' Blocks Are Vulnerabilities for BRCA1 and BRCA2 Deficiency and
Are Reversed by the APE2 Nuclease
. Mol Cell. 2020 Jun 18;78(6):1152-1165.e8.
doi: 10.1016/j.molcel.2020.05.021. Epub 2020 Jun 8. PMID: 32516598.

12: Panda AK, Gangaplara A, Buszko M, Natarajan K, Boyd LF, Sharma S,
Margulies
DH
, Shevach EM. Cutting Edge: Inhibition of the Interaction of NK Inhibitory
Receptors with MHC Class I Augments Antiviral and Antitumor Immunity
. J Immunol.
2020 Jun 29:ji2000412. doi: 10.4049/jimmunol.2000412. Epub ahead of print. PMID:
32601097.

13: Li Z, Li W, Lu M, Bess J Jr, Chao CW, Gorman J, Terry DS, Zhang B, Zhou T,
Blanchard SC,
Kwong PD, Lifson JD, Mothes W, Liu J. Subnanometer structures of
HIV-1 envelope trimers on aldrithiol-2-inactivated virus particles
. Nat Struct
Mol Biol. 2020 Jun 29. doi: 10.1038/s41594-020-0452-2. Epub ahead of print.
PMID: 32601441.

14: Rice PA, Craig NL, Dyda F. Comment on "RNA-guided DNA insertion with CRISPR-
associated transposases"
. Science. 2020 Jun 5;368(6495):eabb2022. doi:
10.1126/science.abb2022. PMID: 32499410.

15: Schmidt T, Louis J,
Clore GM. Probing the interaction between HIV-1 protease
and the homodimeric p66/p66' reverse transcriptase precursor by double electron-
electron resonance EPR spectroscopy
. Chembiochem. 2020 Jun 18. doi:
10.1002/cbic.202000263. Epub ahead of print. PMID: 32558168.

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 - 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)