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Newsletter No. 397
May 20, 2019
Professor Michael Rossmann dies

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

APRIL 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Truong L,
Ferré-D'Amaré AR. From fluorescent proteins to fluorogenic RNAs:
tools for imaging cellular macromolecules
. Protein Sci. 2019 Apr 24. doi:
10.1002/pro.3632. [Epub ahead of print] Review. PubMed PMID: 31017335.

2: Tippana R, Chen MC, Demeshkina NA,
Ferré-D'Amaré AR, Myong S. RNA G-quadruplex
is resolved by repetitive and ATP-dependent mechanism of DHX36
. Nat Commun. 2019
Apr 23;10(1):1855. doi: 10.1038/s41467-019-09802-w. PubMed PMID: 31015431; PubMed
Central PMCID: PMC6478676.

3: Zhou BR, Bai Y. Chromatin structures condensed by linker histones. Essays
Biochem. 2019 Apr 23;63(1):75-87. doi: 10.1042/EBC20180056. Print 2019 Apr 23.
Review. PubMed PMID: 31015384.

4: Matsuda K, Huang J, Zhou T, Sheng Z, Kang BH, Ishida E, Griesman T, Stuccio S,
Bolkhovitinov L, Wohlbold TJ, Chromikova V, Cagigi A, Leung K, Andrews S, Cheung
CSF, Pullano AA, Plyler J, Soto C, Zhang B, Yang Y, Joyce MG, Tsybovsky Y,
Wheatley A, Narpala SR, Guo Y, Darko S, Bailer RT, Poole A, Liang CJ, Smith J,
Alexander J, Gurwith M, Migueles SA, Koup RA, Golding H, Khurana S, McDermott AB,
Shapiro L, Krammer F, Kwong PD, Connors M. Prolonged evolution of the memory B
cell response induced by a replicating adenovirus-influenza H5 vaccine
. Sci
Immunol. 2019 Apr 19;4(34). pii: eaau2710. doi: 10.1126/sciimmunol.aau2710.
PubMed PMID: 31004012.

5: Cheng C, Xu K, Kong R, Chuang GY, Corrigan AR, Geng H, Hill KR, Jafari AJ,
O'Dell S, Ou L, Rawi R, Rowshan AP, Sarfo EK, Sastry M, Saunders KO, Schmidt SD,
Wang S, Wu W, Zhang B, Doria-Rose NA, Haynes BF, Scorpio DG, Shapiro L, Mascola
JR,
Kwong PD. Consistent elicitation of cross-clade HIV-neutralizing responses
achieved in guinea pigs after fusion peptide priming by repetitive envelope
trimer boosting
. PLoS One. 2019 Apr 17;14(4):e0215163. doi:
10.1371/journal.pone.0215163. eCollection 2019. PubMed PMID: 30995238.

6: Trachman RJ 3rd, Autour A, Jeng SCY, Abdolahzadeh A, Andreoni A, Cojocaru R,
Garipov R, Dolgosheina EV, Knutson JR, Ryckelynck M, Unrau PJ,
Ferré-D'Amaré AR.
Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.
Nat Chem Biol. 2019 May;15(5):472-479. doi: 10.1038/s41589-019-0267-9. Epub 2019
Apr 15. PubMed PMID: 30992561.

7: Kanekiyo M, Joyce MG, Gillespie RA, Gallagher JR, Andrews SF, Yassine HM,
Wheatley AK, Fisher BE, Ambrozak DR, Creanga A, Leung K, Yang ES, Boyoglu-Barnum
S, Georgiev IS, Tsybovsky Y, Prabhakaran MS, Andersen H, Kong WP, Baxa U, Zephir
KL, Ledgerwood JE, Koup RA,
Kwong PD, Harris AK, McDermott AB, Mascola JR, Graham
BS. Author Correction: Mosaic nanoparticle display of diverse influenza virus
hemagglutinins elicits broad B cell responses
. Nat Immunol. 2019 Apr 12. doi:
10.1038/s41590-019-0395-0. [Epub ahead of print] PubMed PMID: 30980067.

8: Lu M, Ma X, Castillo-Menendez LR, Gorman J, Alsahafi N, Ermel U, Terry DS,
Chambers M, Peng D, Zhang B, Zhou T, Reichard N, Wang K, Grover JR, Carman BP,
Gardner MR, Nikić-Spiegel I, Sugawara A, Arthos J, Lemke EA, Smith AB 3rd, Farzan
M, Abrams C, Munro JB, McDermott AB, Finzi A,
Kwong PD, Blanchard SC, Sodroski
JG, Mothes W. Associating HIV-1 envelope glycoprotein structures with states on
the virus observed by smFRET
. Nature. 2019 Apr;568(7752):415-419. doi:
10.1038/s41586-019-1101-y. Epub 2019 Apr 10. PubMed PMID: 30971821.

9: O'Brien SP, Swanstrom AE, Pegu A, Ko SY, Immonen TT, Del Prete GQ, Fennessey
CM, Gorman J, Foulds KE, Schmidt SD, Doria-Rose N, Williamson C, Hatziioannou T,
Bieniasz PD, Li H, Shaw GM, Mascola JR, Koup RA,
Kwong PD, Lifson JD, Roederer M,
Keele BF. Rational design and in vivo selection of SHIVs encoding
transmitted/founder subtype C HIV-1 envelopes
. PLoS Pathog. 2019 Apr
3;15(4):e1007632. doi: 10.1371/journal.ppat.1007632. eCollection 2019 Apr. PubMed
PMID: 30943274; PubMed Central PMCID: PMC6447185.

10: Connelly CM, Numata T, Boer RE, Moon MH, Sinniah RS, Barchi JJ, Ferr
é-
D'Amaré
AR, Schneekloth JS Jr. Synthetic ligands for PreQ(1) riboswitches provide
structural and mechanistic insights into targeting RNA tertiary structure
. Nat
Commun. 2019 Apr 2;10(1):1501. doi: 10.1038/s41467-019-09493-3. PubMed PMID:
30940810; PubMed Central PMCID: PMC6445138.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Date Collection with ID22 and Eiger16M

Fred Dyda (NIDDK): During a survey of data collection practices, it became apparent that most users do not take advantage of the current capabilities of ID22 and the Eiger16M. In particular it has been shown that excellent data can collected using 0.2 or 0.25 degrees / 0.05 sec speed so 200 degrees can be collected in 36 or 50 sec. One would of course have to increase transmission, but this should be possible as most people seem to collect at 80 or 90% attenuation. This should be OK, as all indicate that decay is dependent of totla accumulated does and is independent of dose rate.


Detergent-Free Membrane Protein System |  In a newly published paper in PNAS, a team led by Dr. Youzhong Guo of VCU's School of Pharmacy used a new detergent-free method that allowed them to examine the membrane of an Escherichia coli cell, with lipids still in place, providing the clearest view ever of cell membrane that yields unexpected structure. 

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

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 Collection Strategies

 The Fascinating World of Crystallography

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)

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)

 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)