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Newsletter No. 492
 June 19, 2023

ACA News, IUCr Newsletter, IUCr Meetings List

MAY 2023 PUBLICATIONS BY MEMBERS OF THE GROUP 


1: Balaratnam S, Torrey ZR, Calabrese DR, Banco MT, Yazdani K, Liang X,
Fullenkamp CR, Seshadri S, Holewinski RJ, Andresson T, Ferré-D'Amaré AR,
Incarnato D, Schneekloth JS Jr. Investigating the NRAS 5' UTR as a target for
small molecules. Cell Chem Biol. 2023 May 26:S2451-9456(23)00140-X. doi:
10.1016/j.chembiol.2023.05.004. Epub ahead of print. PMID: 37257453.

2: Braun V, Ratliff AC, Celia H, Buchanan SK. Energization of Outer Membrane
Transport by the ExbB ExbD Molecular Motor. J Bacteriol. 2023 May 23:e0003523.
doi: 10.1128/jb.00035-23. Epub ahead of print. PMID: 37219427.

3: Wei E, Bou-Nader C, Perry ML, Fattah R, Zhang J, Leppla SH, Bothra A. S9.6
Antibody-Enzyme Conjugates for the Detection of DNA-RNA Hybrids. Bioconjug Chem.
2023 May 17;34(5):834-844. doi: 10.1021/acs.bioconjchem.2c00609. Epub 2023 Apr
17. PMID: 37194248; PMCID: PMC10197132.

4: Hopper AK, Zhang J. Captured: the elusive eukaryotic tRNA splicing enzyme.
Nat Struct Mol Biol. 2023 May 25. doi: 10.1038/s41594-023-00995-9. Epub ahead of
print. PMID: 37231155.

5: Lee HK, Lee YT, Fan L, Wilt HM, Conrad CE, Yu P, Zhang J, Shi G, Ji X, Wang
YX, Stagno JR. Crystal structure of Escherichia coli thiamine pyrophosphate-
sensing riboswitch in the apo state. Structure. 2023 May
29:S0969-2126(23)00157-0. doi: 10.1016/j.str.2023.05.003. Epub ahead of print.
PMID: 37253356.

6: Passalacqua LFM, Starich MR, Link KA, Wu J, Knutson JR, Tjandra N, Jaffrey
SR, Ferré-D'Amaré AR. Co-crystal structures of the fluorogenic aptamer Beetroot
show that close homology may not predict similar RNA architecture. Nat Commun.
2023 May 23;14(1):2969. doi: 10.1038/s41467-023-38683-3. PMID: 37221204; PMCID:
PMC10205801.

7: Ghosh S, Tugarinov V, Clore GM. Quantitative NMR analysis of the mechanism
and kinetics of chaperone Hsp104 action on amyloid-β42 aggregation and fibril
formation. Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2305823120. doi:
10.1073/pnas.2305823120. Epub 2023 May 15. PMID: 37186848; PMCID: PMC10214214.

8: Hayne CK, Butay KJU, Stewart ZD, Krahn JM, Perera L, Williams JG, Petrovitch
RM, Deterding LJ, Matera AG, Borgnia MJ, Stanley RE. Structural basis for pre-
tRNA recognition and processing by the human tRNA splicing endonuclease complex.
Nat Struct Mol Biol. 2023 May 25. doi: 10.1038/s41594-023-00991-z. Epub ahead of
print. PMID: 37231153.

9: Esser L, Zhou F, Zeher A, Wu W, Huang R, Yu CA, Lane KD, Wellems TE, Xia D.
Structure of Complex III with Bound Antimalarial Agent CK-2-68 Provides Insights
into Selective Inhibition of Plasmodium Cytochrome bc<sub>1</sub> Complexes. J
Biol Chem. 2023 May 24:104860. doi: 10.1016/j.jbc.2023.104860. Epub ahead of
print. PMID: 37236355.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS - Room Temperature Biological Crystallography

 R.E. Thorne, "Determining biomolecular structures near room temperature using X-ray crystallography: conceptes, methods and future optimization"

 R.A. Steiner, "Introduction to the virtual thematic issue on room-temperature biological crystallography"


                            CryoEM: Automating Data Acquisition

 C. Dienemann, "Towards automating single-particle cryo-EM data acquisition"

 A. Cheng et al., "Fully automated multi-grid cryoEM screening using Smart Leginon"

 P.T. Kim et al., "Learning to automate cryo-electron microscopy data collection with Ptolemy"

ARCHIVE: Introduction, Sample Preparation, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Other Biophysical Methods, Integrative Structure Determination.
DISCUSSIONS - Name Change of Our Scientific Interest Group (SIG)?

F. Dyda, X. Ji: In light of rapid advancement of structural biology techniques, we are proposing an SIG name change from "X-ray Diffraction" to either "Structural Biology Methods" or "Structural Biology Techniques." Doing so, our SIG would be listed immediately after the "Structural Biology" SIG in the list of NIH SIGs, showing that our SIG is mainly focused on methods/techniques in structural biology. Please advise with your suggestions.


ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in Crystallography,  Absorption Correction, Data for Refinement and Publication, Validation, Table 1,   Protein Data Bank & Protein Folding.
READINGS AND TUTORIALS - Evolutionay-scale structure prediction

Z. Lin et al., "Evolutionary-scale prediction of atomic-level protein structure with a language model" (2023)

 D.N. Woolfson, "Understanding a protein fold: the physics, chemistry, and biology of alpha-helical coiled coils" (2023)

 G. Huang, C. Zeng, Y. Shi, "Structure of the nuclear pore complex goes atomic" (2023)

 T. Blundell, "Structural Biology, Bioinformatics and Drug Discovery: Six Decades of Science & Its Applications" (2022)


ARCHIVE: Crystallography, Data Aquisition, Structural Biology, Structure Prediction

 LINKS - Suggestions?

Databases: DisProt, ExPASy, HAD, HIC-Up, NDB, PDB, PDBe, Protein Geometry
                  SARS-CoV-2 Related Structures, PDB SARS-CoV-2 Resources, AlphaFold DB,
                  virusMED, BioCyc, RaMP-DB,

Programs: CCP4, COOT, DSSR, HKL, PHENIX, PyMOL, SOLVE, XDS

Servers: ACHESYM, Anisotropy, C6@C3, Dali, ESPript, Grade, PDBePISA, Phyre2,
             MolProbity, RestraintLib, Robetta (RoseTTAFold),

Copyright © NIH X-Ray Diffraction Interest Group                       Maintained by Dr. Xinhua Ji