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Newsletter No. 369
January 15, 2018

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2018, FEBS 2018, Protein Society 2018

DECEMBER 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Luo Z, Dauter Z. The crystal structure of Z-DNA with untypically coordinated
Ca(2+) ions
. J Biol Inorg Chem. 2017 Dec 21. doi: 10.1007/s00775-017-1526-4.
[Epub ahead of print] PubMed PMID: 29270817.

2: Chittori S, Hong J, Saunders H, Feng H, Ghirlando R, Kelly AE, Bai Y,
Subramaniam S. Structural mechanisms of centromeric nucleosome recognition by the
kinetochore protein CENP-N
. Science. 2017 Dec 21. pii: eaar2781. doi:
10.1126/science.aar2781. [Epub ahead of print] PubMed PMID: 29269420.

3: Schmidt T, Tian L, Clore GM. Probing Conformational States of the Finger and
Thumb Subdomains of HIV-1 Reverse Transcriptase Using Double Electron-Electron
Resonance Electron Paramagnetic Resonance Spectroscopy
. Biochemistry. 2017 Dec
21. doi: 10.1021/acs.biochem.7b01035. [Epub ahead of print] PubMed PMID:
29251492.

4: Tang WK, Zhang T, Ye Y, Xia D. Structural basis for nucleotide-modulated p97
association with the ER membrane
. Cell Discov. 2017 Dec 12;3:17045. doi:
10.1038/celldisc.2017.45. eCollection 2017. PubMed PMID: 29238611; PubMed Central
PMCID: PMC5725882.

5: Joyce MG, Georgiev IS, Yang Y, Druz A, Geng H, Chuang GY, Kwon YD, Pancera M,
Rawi R, Sastry M, Stewart-Jones GBE, Zheng A, Zhou T, Choe M, Van Galen JG, Chen
RE, Lees CR, Narpala S, Chambers M, Tsybovsky Y, Baxa U, McDermott AB, Mascola
JR,
Kwong PD. Soluble Prefusion Closed DS-SOSIP.664-Env Trimers of Diverse HIV-1
Strains
. Cell Rep. 2017 Dec 5;21(10):2992-3002. doi:
10.1016/j.celrep.2017.11.016. PubMed PMID: 29212041.

6:
Wlodawer A. Online tools for enhancing presentation, understanding, and
retention of 3D structural data
. FEBS J. 2017 Dec;284(23):3974-3976. doi:
10.1111/febs.14316. PubMed PMID: 29205914.

7:
Dauter Z, Jaskolski M. On the helical arrangements of protein molecules.
Protein Sci. 2017 Dec 1. doi: 10.1002/pro.3356. [Epub ahead of print] PubMed
PMID: 29194829.

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)