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Newsletter No. 382
August 6, 2018

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

JULY 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Natarajan K, Jiang J, May NA, Mage MG, Boyd LF, McShan AC, Sgourakis NG, Bax
A,
Margulies DH. The Role of Molecular Flexibility in Antigen Presentation and T
Cell Receptor-Mediated Signaling
. Front Immunol. 2018 Jul 17;9:1657. doi:
10.3389/fimmu.2018.01657. eCollection 2018. Review. PubMed PMID: 30065727.

2: Dyda F, Rice PA. A new twist on V(D)J recombination. Nat Struct Mol Biol. 2018
Jul 30. doi: 10.1038/s41594-018-0107-8. PubMed PMID: 30061601.

3: Kulinski JM, Metcalfe DD, Young ML, Bai Y, Yin Y, Eisch R, Scott LM, Komarow
HD. Elevation in histamine and tryptase following exercise in patients with
mastocytosis
. J Allergy Clin Immunol Pract. 2018 Jul 23. pii:
S2213-2198(18)30439-2. doi: 10.1016/j.jaip.2018.07.008. PubMed PMID: 30048767.

4: Sekula B, Ruszkowski M, Dauter Z. Structural Analysis of Phosphoserine
Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in
the Phosphorylated Pathway of Serine Biosynthesis
. Front Plant Sci. 2018 Jul
6;9:876. doi: 10.3389/fpls.2018.00876. eCollection 2018. PubMed PMID: 30034403.

5: Kononchik J, Ireland J, Zou Z, Segura J, Holzapfel G, Chastain A, Wang R,
Spencer M, He B, Stutzman N, Kano D, Arthos J, Fischer E, Chun TW, Moir S, Sun P.
HIV-1 targets L-selectin for adhesion and induces its shedding for viral release.
Nat Commun. 2018 Jul 19;9(1):2825. doi: 10.1038/s41467-018-05197-2. PubMed PMID:
30026537.

6: Fashe M, Hashiguchi T, Yi M, Moore R, Negishi M. Phenobarbital-induced
phosphorylation converts nuclear receptor RORα from a repressor to an activator
of the estrogen sulfotransferase gene Sult1e1 in mouse livers
. FEBS Lett. 2018
Jul 19. doi: 10.1002/1873-3468.13199. PubMed PMID: 30025153.

7: Mata CP, Mertens J, Fontana J, Luque D, Allende-Ballestero C, Reguera D, Trus
BL, Steven AC, Carrascosa JL, Castón JR. The RNA-binding protein of a
double-stranded RNA virus acts like a scaffold protein
. J Virol. 2018 Jul 18.
pii: JVI.00968-18. doi: 10.1128/JVI.00968-18. PubMed PMID: 30021893.

8: McShan AC, Natarajan K, Kumirov VK, Flores-Solis D, Jiang J, Badstübner M,
Toor JS, Bagshaw CR, Kovrigin EL, Margulies DH, Sgourakis NG. Peptide exchange on
MHC-I by TAPBPR is driven by a negative allostery release cycle
. Nat Chem Biol.
2018 Jul 9. doi: 10.1038/s41589-018-0096-2. PubMed PMID: 29988068.

9: He P, Yang W. Template and primer requirements for DNA Pol θ-mediated end
joining
. Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7747-7752. doi:
10.1073/pnas.1807329115. Epub 2018 Jul 9. PubMed PMID: 29987024.

10: Kaminski AM, Tumbale PP, Schellenberg MJ,
Williams RS, Williams JG, Kunkel
TA, Pedersen LC, Bebenek K. Structures of DNA-bound human ligase IV catalytic
core reveal insights into substrate binding and catalysis
. Nat Commun. 2018 Jul
6;9(1):2642. doi: 10.1038/s41467-018-05024-8. PubMed PMID: 29980672.

11: Dingens AS, Acharya P, Haddox HK, Rawi R, Xu K, Chuang GY, Wei H, Zhang B,
Mascola JR, Carragher B, Potter CS, Overbaugh J,
Kwong PD, Bloom JD. Complete
functional mapping of infection- and vaccine-elicited antibodies against the
fusion peptide of HIV
. PLoS Pathog. 2018 Jul 5;14(7):e1007159. doi:
10.1371/journal.ppat.1007159. eCollection 2018 Jul. PubMed PMID: 29975771.

12: Banerjee A, Kikuchi Y, Mishkin M, Rauschecker JP, Horwitz B. Chronometry on
Spike-LFP Responses Reveals the Functional Neural Circuitry of Early Auditory
Cortex Underlying Sound Processing and Discrimination
. eNeuro. 2018 Jul 3;5(3).
pii: ENEURO.0420-17.2018. doi: 10.1523/ENEURO.0420-17.2018. eCollection 2018
May-Jun. PubMed PMID: 29971252.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS FSEARCH: cryo-EM Map Replacement

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 DISCUSSIONTable 1

A perspective article "Against Method: Table 1--Cui Bono?" was  recently published in Structure by Bernhard Rupp, pointing out that "Information contained in 'Table 1' is insufficient to evaluate or repeat the experiment, is redundant with information extractable from deposited diffraction data, and includes data items whose meaning is under increased scruitiny in the crystallographic community," and suggesting that "Direct and consistent extraction and analysis of data quality metrics from prefereably unmerged intensity data with graphical presentation of reciprocal space features, including impact on map and model features, should replace 'Table 1'."

Do you agree with Bernhard? Please share your opionion and ideas with fellow crystallographers.

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.

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 (http://mcl1.ncifcrf.gov)