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Newsletter No. 333
May 2, 2016

ACA News, IUCr Newsletter, IUCr Meetings List

 APRIL 2016 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Stewart-Jones GB, Soto C, Lemmin T, Chuang GY, Druz A, Kong R, Thomas PV, Wagh
K, Zhou T, Behrens AJ, Bylund T, Choi CW, Davison JR, Georgiev IS, Joyce MG, Kwon
YD, Pancera M, Taft J, Yang Y, Zhang B, Shivatare SS, Shivatare VS, Lee CD, Wu
CY, Bewley CA, Burton DR, Koff WC, Connors M, Crispin M, Baxa U, Korber BT, Wong
CH, Mascola JR,
Kwong PD. Trimeric HIV-1-Env Structures Define Glycan Shields
from Clades A, B, and G
. Cell. 2016 Apr 21. pii: S0092-8674(16)30401-9. doi:
10.1016/j.cell.2016.04.010. [Epub ahead of print] PubMed PMID: 27114034.

2: Ceccon A, Tugarinov V, Bax A, Clore GM. Global Dynamics and Exchange Kinetics
of a Protein on the Surface of Nanoparticles Revealed by Relaxation-Based
Solution NMR Spectroscopy
. J Am Chem Soc. 2016 Apr 27. [Epub ahead of print]
PubMed PMID: 27111298.

3: Raran-Kurussi S, Waugh DS. A Dual Protease Approach for Expression and
Affinity Purification of Recombinant Proteins
. Anal Biochem. 2016 Apr 19. pii:
S0003-2697(16)30029-X. doi: 10.1016/j.ab.2016.04.006. [Epub ahead of print]
PubMed PMID: 27105777.

4: Bermejo GA, Clore GM, Schwieters CD. Improving NMR Structures of RNA.
Structure. 2016 Apr 2. pii: S0969-2126(16)00085-X. doi:
10.1016/j.str.2016.03.007. [Epub ahead of print] PubMed PMID: 27066747.

5: Mason RD, Welles HC, Adams C, Chakrabarti BK, Gorman J, Zhou T, Nguyen R,
O'Dell S, Lusvarghi S, Bewley CA, Li H, Shaw GM, Sheng Z, Shapiro L, Wyatt R,
Kwong PD, Mascola JR, Roederer M. Targeted Isolation of Antibodies Directed
against Major Sites of SIV Env Vulnerability
. PLoS Pathog. 2016 Apr
11;12(4):e1005537. doi: 10.1371/journal.ppat.1005537. eCollection 2016 Apr.
PubMed PMID: 27064278; PubMed Central PMCID: PMC4827850.

6: Kwon YD, Georgiev IS, Ofek G, Zhang B, Asokan M, Bailer RT, Bao A, Caruso W,
Chen X, Choe M, Druz A, Ko SY, Louder MK, McKee K, O'Dell S, Pegu A, Rudicell R,
Shi W, Wang K, Yang Y, Alger M, Bender MF, Carlton K, Cooper JW, Blinn J,
Eudailey J, Lloyd K, Parks R, Alam SM, Haynes BF, Padte NN, Yu J, Ho DD, Huang J,
Connors M, Schwartz RM, Mascola JR,
Kwong PD. Optimization of the Solubility of
HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based
Design
. J Virol. 2016 Apr 6. pii: JVI.03246-15. [Epub ahead of print] PubMed
PMID: 27053554.

7: Hewitt WM, Lountos GT, Zlotkowski K, Dahlhauser SD, Saunders LB, Needle D,
Tropea JE, Zhan C, Wei G, Ma B, Nussinov R, Waugh DS, Schneekloth JS Jr. Insights
Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9
. Angew Chem Int Ed
Engl. 2016 May 4;55(19):5703-7. doi: 10.1002/anie.201511351. Epub 2016 Apr 1.
PubMed PMID: 27038327.

8: 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; PubMed Central PMCID:
PMC4806563.

9: 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 Apr 7;165(2):449-63. doi: 10.1016/j.cell.2016.02.022. Epub
2016 Mar 3. PubMed PMID: 26949186; PubMed Central PMCID: PMC4826291.

10: Li M, Kandror O, Akopian T, Dharkar P,
Wlodawer A, Maurizi MR, Goldberg AL.
Structure and Functional Properties of the Active Form of the Proteolytic
Complex, ClpP1P2, from Mycobacterium tuberculosis
. J Biol Chem. 2016 Apr
1;291(14):7465-76. doi: 10.1074/jbc.M115.700344. Epub 2016 Feb 8. PubMed PMID:
26858247; PubMed Central PMCID: PMC4817177.

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)