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Newsletter No. 409
November 18, 2019


Portrait of a Crystallographer

ACA News, IUCr Newsletter, IUCr Meetings List

Understanding Biology through Structure, March 16-20, 2020

OCTOBER 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Biancospino M, Buel GR, Niño CA, Maspero E, di Perrotolo RS, Raimondi A,
Redlingshöfer L, Weber J, Brodsky FM, Walters KJ, Polo S. Clathrin light chain A
drives selective myosin VI recruitment to clathrin-coated pits under membrane
tension
. Nat Commun. 2019 Oct 31;10(1):4974. doi: 10.1038/s41467-019-12855-6.
PubMed PMID: 31672988.

2: Park JE, Zhang L, Bang JK, Andresson T, DiMaio F, Lee KS. Phase separation of
Polo-like kinase 4 by autoactivation and clustering drives centriole biogenesis
.
Nat Commun. 2019 Oct 31;10(1):4959. doi: 10.1038/s41467-019-12619-2. PubMed PMID:
31672968.

3: Michael Beyer H, Malgorzata Mikula K, Li M, Wlodawer A, Iwaï H. The crystal
structure of the naturally split gp41-1 intein guides the engineering of
orthogonal split inteins from cis-splicing inteins
. FEBS J. 2019 Oct 30. doi:
10.1111/febs.15113. [Epub ahead of print] PubMed PMID: 31665813.

4: Guo Y, Chen K,
Kwong PD, Shapiro L, Sheng Z. cAb-Rep: A Database of Curated
Antibody Repertoires for Exploring Antibody Diversity and Predicting Antibody
Prevalence
. Front Immunol. 2019 Oct 9;10:2365. doi: 10.3389/fimmu.2019.02365.
eCollection 2019. PubMed PMID: 31649674; PubMed Central PMCID: PMC6794461.

5: Schwieters CD, Bermejo GA, Clore GM. A three-dimensional potential of mean
force to improve backbone and sidechain hydrogen bond geometry in Xplor-NIH
protein structure determination
. Protein Sci. 2019 Oct 15. doi: 10.1002/pro.3745.
[Epub ahead of print] PubMed PMID: 31613020.

6: Ding J, Swain M, Yu P, Stagno JR, Wang YX. Conformational flexibility of
adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free
electron laser
. J Biomol NMR. 2019 Oct 12. doi: 10.1007/s10858-019-00278-w. [Epub
ahead of print] PubMed PMID: 31606878.

7: Rawi R, Mall R, Shen CH, Farney SK, Shiakolas A, Zhou J, Bensmail H, Chun TW,
Doria-Rose NA, Lynch RM, Mascola JR,
Kwong PD, Chuang GY. Accurate Prediction for
Antibody Resistance of Clinical HIV-1 Isolates
. Sci Rep. 2019 Oct 11;9(1):14696.
doi: 10.1038/s41598-019-50635-w. PubMed PMID: 31604961; PubMed Central PMCID:
PMC6789020.

8: Celia H, Botos I, Ni X, Fox T, De Val N, Lloubes R, Jiang J, Buchanan SK.
Cryo-EM structure of the bacterial Ton motor subcomplex ExbB-ExbD provides
information on structure and stoichiometry
. Commun Biol. 2019 Oct 4;2:358. doi:
10.1038/s42003-019-0604-2. eCollection 2019. PubMed PMID: 31602407; PubMed
Central PMCID: PMC6778125.

9: Aguilar OA, Sampaio IS, Rahim MMA, Samaniego JD, Tilahun ME, Krishnamoorthy M,
Popović B, Babić M, Krmpotić A, Treanor B, Margulies DH, Allan DSJ, Makrigiannis
AP, Jonjić S, Carlyle JR. Mouse cytomegalovirus m153 protein stabilizes
expression of the inhibitory NKR-P1B ligand, Clr-b
. J Virol. 2019 Oct 9. pii:
JVI.01220-19. doi: 10.1128/JVI.01220-19. [Epub ahead of print] PubMed PMID:
31597762.

10: Karamanos TK, Tugarinov V,
Clore GM. Unraveling the structure and dynamics of
the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated
proteostasis
. Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21529-21538. doi:
10.1073/pnas.1914999116. Epub 2019 Oct 7. PubMed PMID: 31591220; PubMed Central
PMCID: PMC6815171.

11: Gorman J, Mason RD, Nettey L, Cavett N, Chuang GY, Peng D, Tsybovsky Y,
Verardi R, Nguyen R, Ambrozak D, Biris K, LaBranche CC, Ramesh A, Schramm CA,
Zhou J, Bailer RT, Kepler TB, Montefiori DC, Shapiro L, Douek DC, Mascola JR,
Roederer M,
Kwong PD. Isolation and Structure of an Antibody that Fully
Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan
Shields
. Immunity. 2019 Oct 15;51(4):724-734.e4. doi:
10.1016/j.immuni.2019.09.007. Epub 2019 Oct 2. PubMed PMID: 31586542.

12: Fernandez AJ, Daniel EJP, Mahajan SP, Gray JJ, Gerken TA, Tabak LA, Samara
NL
. The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals
how nonconserved residues dictate its function
. Proc Natl Acad Sci U S A. 2019
Oct 8;116(41):20404-20410. doi: 10.1073/pnas.1902211116. Epub 2019 Sep 23. PubMed
PMID: 31548401; PubMed Central PMCID: PMC6789641.

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.

LECTURES AND TUTORIALS - Data science skills for referees



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"


RIGAKU WEBINAR SERIES (2009 - PRESENT)

LOW RESOLUTION PHASING AND REFINEMENT (2011)

CRYSTALLOGRAPHY: SEEING THINGS IN A DIFFERENT LIGHT (2013)

CRYSTALLOGRAPHY: FOR ASPIRING CRYSTALLOGRAPHERS (2013)

 Data Collection Strategies (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

ACHESYM: AN ALGORITHM AND SERVER FOR STANDARDIZED PLACEMENT OF MACROMOLECULAR MODELS IN THE UNIT CELL (2014)

A GLIMPSE OF STRUCTURAL BIOLOGY THROUGH X-RAY CRYSTALLOGRAPHY (2014)

CRYSTAL CLEAR (2014)

NATIVE SAD IS MATURING (2015)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 Understanding Biology Through Structure (2017)

 The Fascinating World of Crystallography (2018)

Correcting the public record of biological crystallography (2019)


 LINKS - Suggestions?

Databases: BMCDDisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry, Scattering

Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, Phyre, MolProbity, Protein, Robetta Fragment, HHpred,
 
            RestraintLib,


Facilities: 
APS SER-CAT, APS SAXS Capabilities

 
Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (https://mcl1.ncifcrf.gov)