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Newsletter No. 370
February 5, 2018

Congratulations!

Zbigniew Dauter, 2017 Patterson Award Winner!


ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2018, FEBS 2018, Protein Society 2018

JANUARY 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Morellet N, Li X, Wieninger SA, Taylor JL, Bischerour J, Moriau S, Lescop E,
Bardiaux B, Mathy N, Assrir N, Bétermier M, Nilges M, Hickman AB, Dyda F, Craig
NL, Guittet E. Sequence-specific DNA binding activity of the cross-brace zinc
finger motif of the piggyBac transposase
. Nucleic Acids Res. 2018 Jan 27. doi:
10.1093/nar/gky044. [Epub ahead of print] PubMed PMID: 29385532.

2: Frey BF, Jiang J, Sui Y, Boyd LF, Yu B, Tatsuno G, Billeskov R,
Solaymani-Mohammadi S, Berman PW, Margulies DH, Berzofsky JA. Effects of
Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T
Cell Immunity.
J Immunol. 2018 Jan 26. pii: ji1701523. doi:
10.4049/jimmunol.1701523. [Epub ahead of print] PubMed PMID: 29374075.

3: Sekula B, Dauter Z. Crystal structure of thermospermine synthase from Medicago
truncatula and substrate discriminatory features of plant
aminopropyltransferases
. Biochem J. 2018 Jan 24. pii: BCJ20170900. doi:
10.1042/BCJ20170900. [Epub ahead of print] PubMed PMID: 29367265.

4: Deshmukh L, Tugarinov V, Appella DH,
Clore G. Targeting a dark excited state
of HIV-1 nucleocapsid by anti-retroviral thioesters revealed by NMR
. Angew Chem
Int Ed Engl. 2018 Jan 18. doi: 10.1002/anie.201713172. [Epub ahead of print]
PubMed PMID: 29345807.

5: Rana MS, Kumar P, Lee CJ, Verardi R, Rajashankar KR, Banerjee A. Fatty acyl
recognition and transfer by an integral membrane S-acyltransferase
. Science. 2018
Jan 12;359(6372). pii: eaao6326. doi: 10.1126/science.aao6326. PubMed PMID:
29326245.

6: Herschhorn A, Gu C, Moraca F, Ma X, Farrell M, Smith AB 3rd, Pancera M, Kwong
PD
, Schön A, Freire E, Abrams C, Blanchard SC, Mothes W, Sodroski JG. Publisher
Correction: The β20-β21 of gp120 is a regulatory switch for HIV-1 Env
conformational transitions
. Nat Commun. 2018 Jan 8;9(1):158. doi:
10.1038/s41467-017-02463-7. PubMed PMID: 29311557; PubMed Central PMCID:
PMC5758816.

7: Tian L, Kim MS, Li H, Wang J, Yang W. Structure of HIV-1 reverse transcriptase
cleaving RNA in an RNA/DNA hybrid
. Proc Natl Acad Sci U S A. 2018 Jan
16;115(3):507-512. doi: 10.1073/pnas.1719746115. Epub 2018 Jan 2. PubMed PMID:
29295939; PubMed Central PMCID: PMC5777007.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - A Convenient Phasing Vehicle

Zbigniew Dauter (NCI): Selenourea: A Convenient Phasing Vehicle

Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be also inserted into protein crystals in the form of selenourea (SeC(NH2)2), by adding selenourea into mother liquor or cryo-solution or in the form of powder into a drop with native crystals, in analogy to the classic procedure of heavy-atom derivatization. Selenourea is able to bind to reactive groups at the surface of macromolecules primarily through hydrogen bonds, where the selenium atom may serve as acceptor and amide groups as H-bond donors. Selenourea has different chemical properties than other heavy-atom reagents and halide ions and provides a convenient way of phasing crystal structures of macromolecules. A de novo protein crystal structure at low resolution of 2.9 Å with total 1125 residues distributed in seven chains in asymmetric unit at was recently successfully solved with this method. For details, see Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures, Sci. Rep. 6, 37123 (2016) by Zhipu Luo.

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

TOPIC DISCUSSIONMaps, Models, and Structures

Alexander Wlodawer, Mi Li, Zbigniew Dauter
: High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective (PMID: 28867613)
The appearance of ten high-resolution cryoelectron microscopy (cryo-EM) maps of proteins, ribosomes, and viruses was compared with the experimentally phased crystallographic electron density maps of four proteins. We found that maps calculated at a similar resolution by the two techniques are quite comparable in their appearance, although cryo-EM maps, even when sharpened, seem to be a little less detailed. An analysis of models fitted to the cryo-EM maps indicated the presence of significant problems in almost all of them, including incorrect geometry, clashes between atoms, and discrepancies between the map density and the fitted models. In particular, the treatment of the atomic displacement (B) factors was meaningless in almost all analyzed cryo-EM models. Stricter cryo-EM structure deposition standards and their better enforcement are needed.

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.

LECTURES AND TUTORIALS 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 - New Server: RestraintLib
  

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 (http://mcl1.ncifcrf.gov)