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Newsletter No. 364
November 6, 2017

First 3D Movie of a Virus in Action

ACA News, IUCr Newsletter, IUCr Meetings List

OCTOBER 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Prasad R, Çağlayan M, Dai DP, Nadalutti CA, Zhao ML, Gassman NR, Janoshazi AK,
Stefanick DF, Horton JK, Krasich R, Longley MJ, Copeland WC, Griffith JD, Wilson
SH
. DNA polymerase β: A missing link of the base excision repair machinery in
mammalian mitochondria
. DNA Repair (Amst). 2017 Oct 28;60:77-88. doi:
10.1016/j.dnarep.2017.10.011. [Epub ahead of print] PubMed PMID: 29100041.

2: Horton JK, Stefanick DF, Zhao ML, Janoshazi AK, Gassman NR, Seddon HJ, Wilson
SH
. XRCC1-mediated repair of strand breaks independent of PNKP binding. DNA
Repair (Amst). 2017 Oct 19;60:52-63. doi: 10.1016/j.dnarep.2017.10.007. [Epub
ahead of print] PubMed PMID: 29100039.

3: Luo Z,
Dauter Z, Gilski M. Four highly pseudosymmetric and/or twinned
structures of d(CGCGCG)(2) extend the repertoire of crystal structures of Z-DNA
.
Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):940-951. doi:
10.1107/S2059798317014954. Epub 2017 Oct 30. PubMed PMID: 29095165.

4: Deshmukh L, Tugarinov V, Louis JM,
Clore GM. Binding kinetics and substrate
selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by
chemical exchange NMR
. Proc Natl Acad Sci U S A. 2017 Oct 30. pii: 201716098.
doi: 10.1073/pnas.1716098114. [Epub ahead of print] PubMed PMID: 29087351.

5: Sastry M, Zhang B, Chen M, Joyce MG, Kong WP, Chuang GY, Ko K, Kumar A,
Silacci C, Thom M, Salazar AM, Corti D, Lanzavecchia A, Taylor G, Mascola JR,
Graham BS,
Kwong PD. Adjuvants and the vaccine response to the DS-Cav1-stabilized
fusion glycoprotein of respiratory syncytial virus
. PLoS One. 2017 Oct
26;12(10):e0186854. doi: 10.1371/journal.pone.0186854. eCollection 2017. PubMed
PMID: 29073183.

6: Rawi R, Mall R, Kunji K, Shen CH,
Kwong PD, Chuang GY. PaRSnIP: Sequence-Based
Protein Solubility Prediction using Gradient Boosting Machine
. Bioinformatics.
2017 Oct 23. doi: 10.1093/bioinformatics/btx662. [Epub ahead of print] PubMed
PMID: 29069295.

7: Zhao H, Lomash S, Chittori S, Glasser C, Mayer ML, Schuck P. Preferential
assembly of heteromeric kainate and AMPA receptor amino terminal domains
. Elife.
2017 Oct 23;6. pii: e32056. doi: 10.7554/eLife.32056. PubMed PMID: 29058671.

8: Iwaï H, Mikula KM, Oeemig JS, Zhou D, Li M, Wlodawer A. Structural basis for
the persistence of homing endonucleases in transcription factor IIB inteins
. J
Mol Biol. 2017 Oct 18. pii: S0022-2836(17)30498-9. doi:
10.1016/j.jmb.2017.10.016. [Epub ahead of print] PubMed PMID: 29055778.

9: Gumpena R, Lountos GT, Raran-Kurussi S, Tropea JE, Cherry S, Waugh DS. Crystal
structure of the human dual specificity phosphatase 1 catalytic domain
. Protein
Sci. 2017 Oct 20. doi: 10.1002/pro.3328. [Epub ahead of print] PubMed PMID:
29052270.

10: 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. The β20-β21
of gp120 is a regulatory switch for HIV-1 Env conformational transitions
. Nat
Commun. 2017 Oct 19;8(1):1049. doi: 10.1038/s41467-017-01119-w. PubMed PMID:
29051495; PubMed Central PMCID: PMC5648922.

11: Jiang J, Natarajan K, Boyd LF, Morozov GI, Mage MG, Margulies DH. Crystal
structure of a TAPBPR-MHC-I complex reveals the mechanism of peptide editing in
antigen presentation
. Science. 2017 Oct 12. pii: eaao5154. doi:
10.1126/science.aao5154. [Epub ahead of print] PubMed PMID: 29025991.

12: Fyodorov DV, Zhou BR, Skoultchi AI, Bai Y. Emerging roles of linker histones
in regulating chromatin structure and function
. Nat Rev Mol Cell Biol. 2017 Oct
11. doi: 10.1038/nrm.2017.94. [Epub ahead of print] Review. PubMed PMID:
29018282.

13: Yu F, Song H, Wu Y, Chang SY, Wang L, Li W, Hong B, Xia S, Wang C, Khurana S,
Feng Y, Wang Y, Sun Z, He B, Hou D, Manischewitz J, King LR, Song Y, Min JY,
Golding H, Ji X, Lu L, Jiang S, Dimitrov DS, Ying T. A Potent Germline-like Human
Monoclonal Antibody Targets a pH-Sensitive Epitope on H7N9 Influenza
Hemagglutinin
. Cell Host Microbe. 2017 Oct 11;22(4):471-483.e5. doi:
10.1016/j.chom.2017.08.011. Epub 2017 Sep 28. PubMed PMID: 28966056.

14: Liu X, Liang B, Ngwuta J, Liu X, Surman S, Lingemann M, Kwong PD, Graham BS,
Collins PL, Munir S. Attenuated Human Parainfluenza Virus Type 1 Expressing the
Respiratory Syncytial Virus (RSV) Fusion (F) Glycoprotein from an Added Gene:
Effects of Prefusion Stabilization and Packaging of RSV F
. J Virol. 2017 Oct
27;91(22). pii: e01101-17. doi: 10.1128/JVI.01101-17. Print 2017 Nov 15. PubMed
PMID: 28835504; PubMed Central PMCID: PMC5660469.

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.


Xinhua Ji
: It was recently reported that microseeding was used to produce untwinned crystals of an O-demethylase using twinned crystals as seeds (Acta Crystal. F72:897-902, 2016). Microseeding separates nucleation events from crystal growth events so that it can yield different crystal forms. Hence, it is promising that this technique can be used to produce untwinned crystals from twinned seeds.

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.


Mariusz Jaskolski: Pathological Behavior of Atomic Occupancy Factors
A number of PDB files have been detected and reported by Zbyszek Dauter, in which the atomic occupancy factors show a pathological behavior, where covalently connected atoms have uncorrelated fractional occupancies.  This pathology seems to have been spreading unnoticed because MR-generated structures inherited the pathology from some earlier models, and the refinement programs were not rigorous enough to block (or at least signal) the "infection".  You might be advised to check your PDB files for this pathology, using an ad-hoc server http://achesym.ibch.poznan.pl/occucheck/ by Marcin Kowiel.

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 Publication.

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)