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Newsletter No. 422
June 1, 2020

ACA News, IUCr Newsletter, IUCr Meetings List


MAY 2020 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Wlodawer A, Dauter Z, Shabalin I, Gilski M, Brzezinski D, Kowiel M, Minor W,
Rupp B, Jaskolski M. Ligand-centered assessment of SARS-CoV-2 drug target models
in the Protein Data Bank
. FEBS J. 2020 May 17. doi: 10.1111/febs.15366. Epub
ahead of print. PMID: 32418327.

2: Riffault S, Hägglund S, Guzman E, Näslund K, Jouneau L, Dubuquoy C,
Pietralunga V, Laubreton D, Boulesteix O, Gauthier D, Remot A, Boukaridi A, Falk
A, Shevchenko G, Lind SB, Vargmar K, Zhang B,
Kwong PD, Rodriguez MJ, Duran MG,
Schwartz-Cornil I, Eléouët JF, Taylor G, Valarcher JF. A Single Shot Pre-fusion-
Stabilized Bovine RSV F Vaccine is Safe and Effective in Newborn Calves with
Maternally Derived Antibodies
. Vaccines (Basel). 2020 May 18;8(2):E231. doi:
10.3390/vaccines8020231. PMID: 32443437.

3: Lubkowski J, Vanegas J, Chan WK, Lorenzi PL, Weinstein JN, Sukharev S,
Fushman D, Rempe S, Anishkin A, Wlodawer A. Mechanism of Catalysis by
l-Asparaginase
. Biochemistry. 2020 May 26;59(20):1927-1945. doi:
10.1021/acs.biochem.0c00116. Epub 2020 May 11. PMID: 32364696.

4: Margulies DH, Jiang J, Natarajan K. Structural and dynamic studies of TAPBPR
and Tapasin reveal the mechanism of peptide loading of MHC-I molecules
. Curr
Opin Immunol. 2020 May 8;64:71-79. doi: 10.1016/j.coi.2020.04.004. Epub ahead of
print. PMID: 32402827.

5: Sekula B, Ruszkowski M,
Dauter Z. S-adenosylmethionine synthases in plants:
Structural characterization of type I and II isoenzymes from Arabidopsis
thaliana and Medicago truncatula
. Int J Biol Macromol. 2020 May 15;151:554-565.
doi: 10.1016/j.ijbiomac.2020.02.100. Epub 2020 Feb 11. PMID: 32057875.

6: Pillon MC, Goslen KH, Gordon J, Wells ML, Williams JG, Stanley RE. It takes
two (Las1 HEPN endoribonuclease domains) to cut RNA correctly
. J Biol Chem. 2020
May 1;295(18):5857-5870. doi: 10.1074/jbc.RA119.011193. Epub 2020 Mar 27. PMID:
32220933; PMCID: PMC7196650.

7: Sim MJW, Lu J, Spencer M, Hopkins F, Tran E, Rosenberg SA, Long EO,
Sun PD.
High-affinity oligoclonal TCRs define effective adoptive T cell therapy
targeting mutant KRAS-G12D
. Proc Natl Acad Sci U S A. 2020 May 27:201921964.
doi: 10.1073/pnas.1921964117. Epub ahead of print. PMID: 32461371.

8: Beyer HM, Mikula KM, Li M, Wlodawer A, Iwaï H. The crystal structure of the
naturally split gp41-1 intein guides the engineering of orthogonal split inteins
from cis-splicing inteins
. FEBS J. 2020 May;287(9):1886-1898. doi:
10.1111/febs.15113. Epub 2019 Nov 19. PMID: 31665813; PMCID: PMC7190452.

9: Schellenberg MJ, Appel CD, Riccio AA, Butler LR, Krahn JM, Liebermann JA,
Cortés-Ledesma F, Williams RS. Ubiquitin stimulated reversal of topoisomerase 2
DNA-protein crosslinks by TDP2
. Nucleic Acids Res. 2020 May 1:gkaa318. doi:
10.1093/nar/gkaa318. Epub ahead of print. PMID: 32356875.

10: Schmidt T, Jeon J, Okuno Y, Chiliveri SC,
Clore GM. Submillisecond Freezing
Permits Cryoprotectant-Free EPR Double Electron-Electron Resonance Spectroscopy
.
Chemphyschem. 2020 May 7. doi: 10.1002/cphc.202000312. Epub ahead of print.
PMID: 32383308.

11: Chao FA, Khago D, Byrd RA. Achieving pure spin effects by artifact
suppression in methyl adiabatic relaxation experiments
. J Biomol NMR. 2020
May;74(4-5):223-228. doi: 10.1007/s10858-020-00312-2. Epub 2020 Apr 24. PMID:
32333192.

12: Rathore I, Mishra V, Patel C, Xiao H, Gustchina A,
Wlodawer A, Yada RY,
Bhaumik P. Activation mechanism of plasmepsins, pepsin-like aspartic proteases
from Plasmodium, follows a unique trans-activation pathway
. FEBS J. 2020 May 9.
doi: 10.1111/febs.15363. Epub ahead of print. PMID: 32385863.

13: Trachman RJ 3rd, Cojocaru R, Wu D, Piszczek G, Ryckelynck M, Unrau PJ,
Ferré-D'Amaré AR. Structure-Guided Engineering of the Homodimeric Mango-IV
Fluorescence Turn-on Aptamer Yields an RNA FRET Pair
. Structure. 2020 May
1:S0969-2126(20)30126-X. doi: 10.1016/j.str.2020.04.007. Epub ahead of print.
PMID: 32386573.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Contributions?

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

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.

READINGS AND TUTORIALS - XFEL vs microED (Link)


Methods Comparison: XFEL vs microED (2020)

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"


LOW RESOLUTION PHASING AND REFINEMENT (2011)

 Data Collection Strategies (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

CRYSTAL CLEAR (2014)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 Understanding Biology Through Structure (2017)

 On the state of crystallography at the dawn of the electron microscopy revolution (2017)

 The Fascinating World of Crystallography (2018)

 Data science skills for referees: I biological X-ray crystallography  (2018)

Correcting the public record of biological crystallography (2019)

A Little Dictionary of Crystallography (2019)

Early history of cryo-cooling for macromolecular crystallography (2019)

 LINKS SARS-CoV-2 Related Structures (Link)

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry
                  SARS-CoV-2 Related Structures,


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


Servers: ACHESYM,
Anisotropy, C6@C3, DaliESPript, Grade, PDBePISA, Phyre2,
             MolProbity, RestraintLib,

Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (https://mcl1.ncifcrf.gov)