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Newsletter No. 332
April 18, 2016

ACA News, IUCr Newsletter, IUCr Meetings List

MARCH 2016 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Kim T, Freudenthal BD, Beard WA, Wilson SH, Schlick T. Insertion of oxidized
nucleotide triggers rapid DNA polymerase opening
. Nucleic Acids Res. 2016 Mar 31.
pii: gkw174. PubMed PMID: 27034465.

2: Leal AR, Cruz R, Bur D, Huesgen PF, Faro R, Manadas B,
Wlodawer A, Faro C,
Simões I. Enzymatic properties, evidence for in vivo expression, and
intracellular localization of shewasin D, the pepsin homolog from Shewanella
denitrificans
. Sci Rep. 2016 Mar 31;6:23869. PubMed PMID: 27029611.

3: Shivatare SS, Chang SH, Tsai TI, Tseng SY, Shivatare VS, Lin YS, Cheng YY, Ren
CT, Lee CC, Pawar S, Tsai CS, Shih HW, Zeng YF, Liang CH, Kwong PD, Burton DR, Wu
CY, Wong CH. Modular synthesis of N-glycans and arrays for the hetero-ligand
binding analysis of HIV antibodies
. Nat Chem. 2016 Apr;8(4):338-46. doi:
10.1038/nchem.2463. Epub 2016 Mar 7. PubMed PMID: 27001729.

4: Bonsignori M, Zhou T, Sheng Z, Chen L, Gao F, Joyce MG, Ozorowski G, Chuang
GY, Schramm CA, Wiehe K, Alam SM, Bradley T, Gladden MA, Hwang KK, Iyengar S,
Kumar A, Lu X, Luo K, Mangiapani MC, Parks RJ, Song H, Acharya P, Bailer RT, Cao
A, Druz A, Georgiev IS, Kwon YD, Louder MK, Zhang B, Zheng A, Hill BJ, Kong R,
Soto C; NISC Comparative Sequencing Program, Mullikin JC, Douek DC, Montefiori
DC, Moody MA, Shaw GM, Hahn BH, Kelsoe G, Hraber PT, Korber BT, Boyd SD, Fire AZ,
Kepler TB, Shapiro L, Ward AB, Mascola JR, Liao HX,
Kwong PD, Haynes BF.
Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic
Antibody
. Cell. 2016 Mar 2. pii: PubMed PMID: 26949186.

5: Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C,
Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ,
Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD,
Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF,
Fan QR, Ferré-D'Amaré AR, Christopher Fromme J, Garcia KC, Gaudet R, Gong P,
Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS,
Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport
TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y,
Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser
JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data
publication with the structural biology data grid supports live analysis
. Nat
Commun. 2016 Mar 7;7:10882. PubMed PMID: 26947396.

6:
Xia D, Tang WK, Ye Y. Structure and function of the AAA+ ATPASE p97/Cdc48p.
Gene. 2016 Mar 3. pii: S0378-1119(16)30125-1. doi: 10.1016/j.gene.2016.02.042.
Review. PubMed PMID: 26945625.

7: Singh K, Gittis AG, Gitti RK, Ostazeski SA, Su HP, Garboczi DN. The vaccinia
virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a
glycosyltransferase fold and binds UDP-Glucose
. J Virol. 2016 Mar 2. pii:
JVI.02933-15. PubMed PMID: 26937025.

8: Grabundzija I, Messing SA, Thomas J, Cosby RL, Bilic I, Miskey C, Gogol-Döring
A, Kapitonov V, Diem T, Dalda A, Jurka J, Pritham EJ, Dyda F, Izsvák Z, Ivics Z.
A Helitron transposon reconstructed from bats reveals a novel mechanism of genome
shuffling in eukaryotes
. Nat Commun. 2016 Mar 2;7:10716. PubMed PMID: 26931494.

9: Morgand M, Bouvin-Pley M, Plantier JC, Moreau A, Alessandri E, Simon F, Pace
CS, Pancera M, Ho DD, Poignard P, Bjorkman PJ, Mouquet H, Nussenzweig MC,
Kwong PD, Baty D, Chames P, Braibant M, Barin F. V1/V2 Neutralizing Epitope is
Conserved in Divergent Non-M Groups of HIV-1
. J Acquir Immune Defic Syndr. 2016
Mar 1;71(3):237-45. PubMed PMID: 26413851.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS AND METHODS - Widening the Reach of Structural Biology

X-ray free electron laser (XFEL) features stobe-like pulses that are just a few millionths of a billionth of a second long and a billion times brighter than synchrotron X-ray. The Linac Coherent Light Source (LCLS), operated by Stanford University for the U.S. Department of Energy, is the world's first XFEL facility, where scientists take crisp pictures of atomic motions, watch chemical reactions unfold, probe the properties of materials, and explore fundamental processes in living things. Its performance over the first five years of operation has already provided a breathtaking array of world-leading results.

Micro-electron diffraction (MicroED) data is collected from small 3D microcrystals  using a very low electron dose and readily processed using MOSFLM. Using the MicroED approach, the structure of lysozyme was solved using at 2.5-angstrom resolution (PDB entry 3J6K)  and  the structure of the toxic core of alpha-synuclein was determined at 1.4-angstrom resolution (PDB entry 4RIL). For a review, please see Protein structure determination by MicroED.

Cryo-electron microscopy (CryoEM) is an ensemble of techniques allowing the observation of biological specimens in their native environment at cryogenic temperatures in EM. For a recent cryoEM structure at high resolution, please see 2.2 Å resolution cryo-EM structure of b-galactosidase in complex with a cell-permeant inhibitor. For an overview, please see CryoEM at IUCrJ: a new era.

Small-angle X-ray scattering (SAXS) is capable of delivering structural information of biological macromolecules and their complexes in solution, small or large. For a recent example, the SAXS model for a ~500-kDa RapA:RNA polymerase complex (~230 angstroms in its longest dimension), please see Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA Polymerase: Biochemical and Structural Studies.

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

TOPIC DISCUSSIONCrystal Structures

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.

Mariusz Jaskolski: Geometrical Restraints of His Residues
A recent paper, already listed on this bulletin board, will give you a hint about improving the geometrical restraints of His residues, depending on their protonation/tautomeric form, especially at high resolution:

M.Malinska, M.Dauter, M.Kowiel, M.Jaskolski, Z.Dauter (2015) Protonation and geometry of histidine rings. Acta Cryst. D71, 1444-1454.

This may be a good occasion to mention that for years Refmac has been using the older (1991) version (containing errors) of the Engh & Huber stereochemical dictionary, even though the authors themselves (E&H) corrected it in 2001...

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, Structural Genomics, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and Publication.

LECTURES AND TUTORIALS - Dr. Dauter's Lectures Are Back!

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)

NATIVE SAD IS MATURING (2015)

 LINKS - Suggestions?     

Databases: BMCD, CryoD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry Database, Scattering

Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, USF, XDS


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, PhyreProbity, Protein, Robetta Fragment & HHpred  

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)