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Newsletter No. 323
November 2, 2015

ACA News, IUCr Newsletter, IUCr Meetings List

OCTOBER 2015 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Pegu A, Asokan M, Wu L, Wang K, Hataye J, Casazza JP, Guo X, Shi W, Georgiev
I, Zhou T, Chen X, O'Dell S, Todd JP,
Kwong PD, Rao SS, Yang ZY, Koup RA, Mascola
JR, Nabel GJ. Activation and lysis of human CD4 cells latently infected with
HIV-1.
Nat Commun. 2015 Oct 20;6:8447. PubMed PMID: 26485194.

2: Doria-Rose NA, Bhiman JN, Roark RS, Schramm CA, Gorman J, Chuang GY, Pancera
M, Cale EM, Ernandes MJ, Louder MK, Asokan M, Bailer RT, Druz A, Fraschilla IR,
Garrett NJ, Jarosinski M, Lynch RM, McKee K, O'Dell S, Pegu A, Schmidt SD, Staupe
RP, Sutton MS, Wang K, Wibmer CK, Haynes BF, Abdool-Karim S, Shapiro L,
Kwong PD,
Moore PL, Morris L, Mascola JR. A new member of the V1V2-directed CAP256-VRC26
lineage that shows increased breadth and exceptional potency.
J Virol. 2015 Oct
14. pii: JVI.01791-15. PubMed PMID: 26468542.

3: Ngwuta JO, Chen M, Modjarrad K, Joyce MG, Kanekiyo M, Kumar A, Yassine HM,
Moin SM, Killikelly AM, Chuang GY, Druz A, Georgiev IS, Rundlet EJ, Sastry M,
Stewart-Jones GB, Yang Y, Zhang B, Nason MC, Capella C, Peeples ME, Ledgerwood
JE, McLellan JS,
Kwong PD, Graham BS. Prefusion F-specific antibodies determine
the magnitude of RSV neutralizing activity in human sera.
Sci Transl Med. 2015
Oct 14;7(309):309ra162. PubMed PMID: 26468324.

4: Alberstein R, Grey R, Zimmet A, Simmons DK, Mayer ML. Glycine activated ion
channel subunits encoded by ctenophore glutamate receptor genes.
Proc Natl Acad
Sci U S A. 2015 Oct 12. PubMed PMID: 26460032.

5: Bhiman JN, Anthony C, Doria-Rose NA, Karimanzira O, Schramm CA, Khoza T,
Kitchin D, Botha G, Gorman J, Garrett NJ, Abdool Karim SS, Shapiro L, Williamson
C,
Kwong PD, Mascola JR, Morris L, Moore PL. Viral variants that initiate and
drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies.
Nat Med.
2015 Oct 12. PubMed PMID: 26457756.

6: Li M, Gustchina A, Cruz R, Simões M, Curto P, Martinez J, Faro C, Simões I,
Wlodawer A. Structure of RC1339/APRc from Rickettsia conorii, a retropepsin-like
aspartic protease.
Acta Crystallogr D Biol Crystallogr. 2015 Oct 1;71(Pt
10):2109-18. PubMed PMID: 26457434.

7: Asokan M, Rudicell RS, Louder M, McKee K, O'Dell S, Stewart-Jones G, Wang K,
Xu L, Chen X, Choe M, Chuang G, Georgiev IS, Joyce MG, Kirys T, Ko S, Pegu A, Shi
W, Todd JP, Yang Z, Bailer RT, Rao S,
Kwong PD, Nabel GJ, Mascola JR. Bispecific
antibodies targeting different epitopes on the HIV-1 envelope exhibit broad and
potent neutralization.
J Virol. 2015 Oct 7. PubMed PMID: 26446600.

8: O'Neil PK, Rollauer SE, Noinaj N,
Buchanan SK. Fitting the Pieces of the
β-Barrel Assembly Machinery Complex.
Biochemistry. 2015 Oct 20;54(41):6303-11.
doi: 10.1021/acs.biochem.5b00852. PubMed PMID: 26394220.

9: Rollauer SE, Sooreshjani MA, Noinaj N,
Buchanan SK. Outer membrane protein
biogenesis in Gram-negative bacteria.
Philos Trans R Soc Lond B Biol Sci. 2015
Oct 5;370(1679). pii: 20150023. Review. PubMed PMID: 26370935.

10: Kuszak AJ, Jacobs D, Gurnev PA, Shiota T, Louis JM, Lithgow T, Bezrukov SM,
Rostovtseva TK,
Buchanan SK. Evidence of Distinct Channel Conformations and
Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein
Translocase Pore Tom40.
J Biol Chem. 2015 Oct 23;290(43):26204-17.
PubMed PMID: 26336107.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS - SAXS (small-angle X-ray scattering)

Small-angle X-ray scattering (SAXS) is capable of delivering structural information of biological macromolecules and their complexes in solution, small or large. For a recent example, the SAXS model for a ~500-kDa RapA:RNA polymerase complex (~230 angstroms in its longest dimension), please see Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA Polymerase: Biochemical and Structural Studies.

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation.

TOPIC DISCUSSION - Suggestions?

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, Structural Genomics, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and Publication.

LECTURES AND TUTORIALS - Dr. Dauter's Lectures Are Back!

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)

 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)

NATIVE SAD IS MATURING (2015)

 LINKS - Suggestions?     

Databases: BMCD, CryoD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry Database, Scattering

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


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, PhyreProbity, Protein, Robetta Fragment & HHpred  

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 (http://mcl1.ncifcrf.gov)