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Newsletter No. 363
October 16, 2017

First 3D Movie of a Virus in Action

ACA News, IUCr Newsletter, IUCr Meetings List

SEPTEMBER 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Wälti MA, Clore GM. Disassembly/reassembly strategy for the production of
highly pure GroEL, a tetradecameric supramolecular machine, suitable for
quantitative NMR, EPR and mutational studies
. Protein Expr Purif. 2017 Sep 22.
pii: S1046-5928(17)30448-5. doi: 10.1016/j.pep.2017.09.010. [Epub ahead of print]
PubMed PMID: 28951283.

2: Amano M, Miguel Salcedo-Gómez P, Yedidi RS, Delino NS, Nakata H, Venkateswara
Rao K, Ghosh AK, Mitsuya H. GRL-09510, a Unique
P2-Crown-Tetrahydrofuranylurethane -Containing HIV-1 Protease Inhibitor,
Maintains Its Favorable Antiviral Activity against Highly-Drug-Resistant HIV-1
Variants in vitro
. Sci Rep. 2017 Sep 25;7(1):12235. doi:
10.1038/s41598-017-12052-9. PubMed PMID: 28947797.

3: Warner KD, Sjekloća L, Song W, Filonov GS, Jaffrey SR, Ferré-D'Amaré AR. A
homodimer interface without base pairs in an RNA mimic of red fluorescent
protein
. Nat Chem Biol. 2017 Sep 25. doi: 10.1038/nchembio.2475. [Epub ahead of
print] PubMed PMID: 28945234.

4: Xu L, Pegu A, Rao E, Doria-Rose N, Beninga J, McKee K, Lord DM, Wei RR, Deng
G, Louder M, Schmidt SD, Mankoff Z, Wu L, Asokan M, Beil C, Lange C, Leuschner
WD, Kruip J, Sendak R, Do Kwon Y, Zhou T, Chen X, Bailer RT, Wang K, Choe M,
Tartaglia LJ, Barouch DH, O'Dell S, Todd JP, Burton DR, Roederer M, Connors M,
Koup RA,
Kwong PD, Yang ZY, Mascola JR, Nabel GJ. Trispecific broadly
neutralizing HIV antibodies mediate potent SHIV protection in macaques
. Science.
2017 Sep 20. pii: eaan8630. doi: 10.1126/science.aan8630. [Epub ahead of print]
PubMed PMID: 28931639.

5: Pillon MC, Stanley RE. Nuclease integrated kinase super assemblies (NiKs) and
their role in RNA processing
. Curr Genet. 2017 Sep 19. doi:
10.1007/s00294-017-0749-9. [Epub ahead of print] Review. PubMed PMID: 28929238.

6: Bhandari YR, Fan L, Fang X, Zaki G, Stahlberg EA, Jiang W, Schwieters CD,
Stagno JR,
Wang YX. Topological structure determination of RNA using small angle
X-ray scattering
. J Mol Biol. 2017 Sep 13. pii: S0022-2836(17)30428-X. doi:
10.1016/j.jmb.2017.09.006. [Epub ahead of print] PubMed PMID: 28918093.

7: Schellenberg MJ, Lieberman JA, Herrero-Ruiz A, Butler LR, Williams JG,
Muñoz-Cabello AM, Mueller GA, London RE, Cortés-Ledesma F, Williams RS. ZATT
(ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links
. Science.
2017 Sep 14. pii: eaam6468. doi: 10.1126/science.aam6468. [Epub ahead of print]
PubMed PMID: 28912134.

8: Gotoh S, Miyauchi Y, Moore R, Negishi M. Glucose elicits serine/threonine
kinase VRK1 to phosphorylate nuclear pregnane X receptor as a novel hepatic
gluconeogenic signal
. Cell Signal. 2017 Sep 12;40:200-209. doi:
10.1016/j.cellsig.2017.09.003. [Epub ahead of print] PubMed PMID: 28911860.

9: Rodriguez Y, Howard MJ, Cuneo MJ, Prasad R,
Wilson SH. Unencumbered Pol β
lyase activity in nucleosome core particles
. Nucleic Acids Res. 2017 Sep
6;45(15):8901-8915. doi: 10.1093/nar/gkx593. PubMed PMID: 28911106; PubMed
Central PMCID: PMC5587807.

10: Julg B, Tartaglia LJ, Keele BF, Wagh K, Pegu A, Sok D, Abbink P, Schmidt SD,
Wang K, Chen X, Joyce MG, Georgiev IS, Choe M,
Kwong PD, Doria-Rose NA, Le K,
Louder MK, Bailer RT, Moore PL, Korber B, Seaman MS, Abdool Karim SS, Morris L,
Koup RA, Mascola JR, Burton DR, Barouch DH. Broadly neutralizing antibodies
targeting the HIV-1 envelope V2 apex confer protection against a clade C SHIV
challenge
. Sci Transl Med. 2017 Sep 6;9(406). pii: eaal1321. doi:
10.1126/scitranslmed.aal1321. PubMed PMID: 28878010.

11: Ruszkowski M, Dauter Z. Structures of Medicago truncatula L-Histidinol
Dehydrogenase Show Rearrangements Required for NAD(+) Binding and the Cofactor
Positioned to Accept a Hydride
. Sci Rep. 2017 Sep 5;7(1):10476. doi:
10.1038/s41598-017-10859-0. PubMed PMID: 28874718; PubMed Central PMCID:
PMC5585171.

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 DISCUSSION - Maps, 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 crystal structures in the PDB 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)