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Newsletter No. 314
June 1, 2015

 

Dr. Alexander Wlodawer and Dr. Mariusz Jaskolski were selected to receive the prestigious Poland - U.S. Science Award newly established by the Foundation for Polish Science and the American Association for the Advancement of Science. Congratulations!

ACA News, IUCr Newsletter, IUCr Meetings List

MAY 2015 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Crooks ET, Tong T, Chakrabarti B, Narayan K, Georgiev IS, Menis S, Huang X,
Kulp D, Osawa K, Muranaka J, Stewart-Jones G, Destefano J, O'Dell S, LaBranche C,
Robinson JE, Montefiori DC, McKee K, Du SX, Doria-Rose N,
Kwong PD, Mascola JR,
Zhu P, Schief WR, Wyatt RT, Whalen RG, Binley JM. Vaccine-Elicited Tier 2 HIV-1
Neutralizing Antibodies Bind to Quaternary Epitopes Involving Glycan-Deficient
Patches Proximal to the CD4 Binding Site. PLoS Pathog. 2015 May
29;11(5):e1004932. doi: 10.1371/journal.ppat.1004932. eCollection 2015 May.
PubMed PMID: 26023780.

2: Zhou T, Lynch RM, Chen L, Acharya P, Wu X, Doria-Rose NA, Joyce MG, Lingwood
D, Soto C, Bailer RT, Ernandes MJ, Kong R, Longo NS, Louder MK, McKee K, O'Dell
S, Schmidt SD, Tran L, Yang Z, Druz A, Luongo TS, Moquin S, Srivatsan S, Yang Y,
Zhang B, Zheng A, Pancera M, Kirys T, Georgiev IS, Gindin T, Peng HP, Yang AS;
NISC Comparative Sequencing Program, Mullikin JC, Gray MD, Stamatatos L, Burton
DR, Koff WC, Cohen MS, Haynes BF, Casazza JP, Connors M, Corti D, Lanzavecchia A,
Sattentau QJ, Weiss RA, West AP Jr, Bjorkman PJ, Scheid JF, Nussenzweig MC,
Shapiro L, Mascola JR,
Kwong PD. Structural Repertoire of HIV-1-Neutralizing
Antibodies Targeting the CD4 Supersite in 14 Donors. Cell. 2015 May 20. pii:
S0092-8674(15)00554-1. doi: 10.1016/j.cell.2015.05.007. PubMed PMID: 26004070.

3: Shingai M, Welbourn S, Brenchley JM, Acharya P, Miyagi E, Plishka RJ,
Buckler-White A,
Kwong PD, Nishimura Y, Strebel K, Martin MA. The Expression of
Functional Vpx during Pathogenic SIVmac Infections of Rhesus Macaques Suppresses
SAMHD1 in CD4+ Memory T Cells. PLoS Pathog. 2015 May 21;11(5):e1004928. doi:
10.1371/journal.ppat.1004928. eCollection 2015 May. PubMed PMID: 25996507.

4: Gassman NR, Wilson SH. Micro-irradiation tools to visualize base excision
repair and single-strand break repair. DNA Repair (Amst). 2015 May 5;31:52-63.
doi: 10.1016/j.dnarep.2015.05.001. Review. PubMed PMID: 25996408.

5: Thapar R. Roles of Prolyl Isomerases in RNA-Mediated Gene Expression.
Biomolecules. 2015 May 18;5(2):974-999. Review. PubMed PMID: 25992900.

6: Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson SH, Goodman MF, McKenna
CE. Two Scaffolds from Two Flips: (α,β)/(β,γ) CH(2)/NH "Met-Im" Analogues of
dTTP. Org Lett. 2015 May 13. [Epub ahead of print] PubMed PMID: 25970636.

7: Zhang J,
Ferré-D'Amaré AR. Structure and mechanism of the T-box riboswitches.
Wiley Interdiscip Rev RNA. 2015 May 8. doi: 10.1002/wrna.1285. [Epub ahead of
print] PubMed PMID: 25959893.

8: Needle D, Lountos GT, Waugh DS. Structures of the Middle East respiratory
syndrome coronavirus 3C-like protease reveal insights into substrate specificity.
Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1102-11. doi:
10.1107/S1399004715003521. Epub 2015 Apr 24. PubMed PMID: 25945576.

9: Liu B, Chen W, Natarajan K, Li Z, Margulies DH, Zhu C. The cellular
environment regulates in situ kinetics of T-cell receptor interaction with
peptide major histocompatibility complex. Eur J Immunol. 2015 May 6. doi:
10.1002/eji.201445358. [Epub ahead of print] PubMed PMID: 25944482.

10: Liu Y, Holmstrom E, Zhang J, Yu P, Wang J, Dyba MA, De Chen, Ying J, Lockett
S, Nesbitt DJ,
Ferré-D'Amaré AR, Sousa R, Stagno JR, Wang YX. Synthesis and
applications of RNAs with position-selective labelling and mosaic composition.
Nature. 2015 May 4. doi: 10.1038/nature14352. PubMed PMID: 25938715.

11: Chuang GY, Zhang B, McKee K, O'Dell S, Kwon YD, Zhou T, Blinn J, Lloyd K,
Parks R, Von Holle T, Ko SY, Kong WP, Pegu A, Wang K, Baruah K, Crispin M,
Mascola JR, Moody MA, Haynes BF, Georgiev IS,
Kwong PD. Eliminating antibody
polyreactivity through addition of N-linked glycosylation. Protein Sci. 2015
Jun;24(6):1019-30. doi: 10.1002/pro.2682. PubMed PMID: 25800131.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS - Contributions?  (Click for PDF reader to view articles)


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 - Suggestions?

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 BY KEVIN COWTAN (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

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

 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)