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Newsletter No. 392
February 18, 2019

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

JANUARY 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Lo YH, Sobhany M, Hsu AL, Ford BL, Krahn JM, Borgnia MJ, Stanley RE. Cryo-EM
structure of the essential ribosome assembly AAA-ATPase Rix7
. Nat Commun. 2019
Jan 31;10(1):513. doi: 10.1038/s41467-019-08373-0. PubMed PMID: 30705282.

2: Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W. Structures and
operating principles of the replisome.
Science. 2019 Jan 24. pii: eaav7003. doi:
10.1126/science.aav7003. [Epub ahead of print] PubMed PMID: 30679383.

3: Ruszkowski M, Dauter Z. Comment on Wang's paper on the covalent Cys-X-Lys
bridges
. Protein Sci. 2019 Jan 21. doi: 10.1002/pro.3576. [Epub ahead of print]
PubMed PMID: 30666728.

4: Chen X, Ebelle DL, Wright BJ, Sridharan V, Hooper E, Walters KJ. Structure of
hRpn10 Bound to UBQLN2 UBL Illustrates Basis for Complementarity between Shuttle
Factors and Substrates at the Proteasome
. J Mol Biol. 2019 Jan 18. pii:
S0022-2836(19)30030-0. doi: 10.1016/j.jmb.2019.01.021. [Epub ahead of print]
PubMed PMID: 30664872.

5: Smith MR, Shock DD, Beard WA, Greenberg MM, Freudenthal BD, Wilson SH. A
guardian residue hinders insertion of a Fapy•dGTP analog by modulating the
open-closed DNA polymerase transition
. Nucleic Acids Res. 2019 Jan 16. doi:
10.1093/nar/gkz002. [Epub ahead of print] PubMed PMID: 30649431.

6: Li M, Srp J, Gustchina A,
Dauter Z, Mares M, Wlodawer A. Crystal structures of
the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and
modeling of kallikrein complexes
. Acta Crystallogr D Struct Biol. 2019 Jan
1;75(Pt 1):56-69. doi: 10.1107/S2059798318016492. Epub 2019 Jan 7. PubMed PMID:
30644845; PubMed Central PMCID: PMC6333282.

7: Hogan M, Bahta M, Tsuji K, Nguyen TX, Cherry S, Lountos GT, Tropea JE, Zhao
BM, Zhao XZ, Waugh DS, Burke TR Jr, Ulrich RG. Targeting Protein-Protein
Interactions of Tyrosine Phosphatases with Microarrayed Fragment Libraries
Displayed on Phosphopeptide Substrate Scaffolds
. ACS Comb Sci. 2019 Jan 31. doi:
10.1021/acscombsci.8b00122. [Epub ahead of print] PubMed PMID: 30629404.

8: Bofill-De Ros X, Kasprzak WK, Bhandari Y, Fan L, Cavanaugh Q, Jiang M, Dai L,
Yang A, Shao TJ, Shapiro BA, Wang YX, Gu S. Structural Differences between
Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target
Repertoires
. Cell Rep. 2019 Jan 8;26(2):447-459.e4. doi:
10.1016/j.celrep.2018.12.054. PubMed PMID: 30625327.

9: Thornton AM, Lu J, Korty PE, Kim YC, Martens C, Sun PD, Shevach EM. Helios(+)
and Helios(-) Treg subpopulations are phenotypically and functionally distinct
and express dissimilar TCR repertoires
. Eur J Immunol. 2019 Jan 8. doi:
10.1002/eji.201847935. [Epub ahead of print] PubMed PMID: 30620397.

10: Lai YT, Wang T, O'Dell S, Louder MK, Schön A, Cheung CSF, Chuang GY, Druz A,
Lin B, McKee K, Peng D, Yang Y, Zhang B, Herschhorn A, Sodroski J, Bailer RT,
Doria-Rose NA, Mascola JR, Langley DR,
Kwong PD. Lattice engineering enables
definition of molecular features allowing for potent small-molecule inhibition of
HIV-1 entry
. Nat Commun. 2019 Jan 3;10(1):47. doi: 10.1038/s41467-018-07851-1.
PubMed PMID: 30604750; PubMed Central PMCID: PMC6318274.

11: Yost SA, Whidby J, Khan AG, Wang Y,
Marcotrigiano J. Overcoming Challenges of
Hepatitis C Virus Envelope Glycoprotein Production in Mammalian Cells
. Methods
Mol Biol. 2019;1911:305-316. doi: 10.1007/978-1-4939-8976-8_21. PubMed PMID:
30593635.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS New Detergent-Free System for Membrane                                                                         Protein Structural Biology

Detergent-Free Membrane Protein System |  In a newly published paper in PNAS, a team led by Dr. Youzhong Guo of VCU's School of Pharmacy used a new detergent-free method that allowed them to examine the membrane of an Escherichia coli cell, with lipids still in place, providing the clearest view ever of cell membrane that yields unexpected structure. 

FSEARCH: cryo-EM Map Replacement |  Recently, a  hybrid method that integrates X-ray crystallography with cryo-EM for structure determination is presented by Lingxiao Zeng, Wei Ding, and Quan Hao in the IUCrJ (5:382-389, 2018). The starting point is a cryo-EM map  and the end point is a high-resolution crystal structure. The workflow of the method and four case study examples can be seen here.

A new MR-SAD algorithm | 
Recently, a  new MR-SAD algorithm was  reported  by Pavol Skubak, Navray Pannu, and co-workers in the IUCrJ (5:166-171, 2018), for automatic building of protein models from low-resolution X-ray diffraction data and a poor starting model. According to the authors, their algorithm uses a multivariate function to simultatnerously exploit informatino from both the initial partial model and low-resolution SAD data. Details of the algorithm and its application to six challenging structure determinations can be seen here.

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

TOPIC DISCUSSIONSuggestions?

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, Table 1.

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 - Suggestions?

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 (https://mcl1.ncifcrf.gov)