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Newsletter No. 493
 July 3, 2023

ACA News, IUCr Newsletter, IUCr Meetings List

JUNE 2023 PUBLICATIONS BY MEMBERS OF THE GROUP 


1: Passalacqua LFM, Banco MT, Moon JD, Li X, Jaffrey SR, Ferré-D'Amaré AR.
Intricate 3D architecture of a DNA mimic of GFP. Nature. 2023
Jun;618(7967):1078-1084. doi: 10.1038/s41586-023-06229-8. Epub 2023 Jun 21.
PMID: 37344591.

2: Shindo S, Kakizaki S, Sakaki T, Kawasaki Y, Sakuma T, Negishi M, Shizu R.
Phosphorylation of nuclear receptors: Novelty and therapeutic implications.
Pharmacol Ther. 2023 Jun 15;248:108477. doi: 10.1016/j.pharmthera.2023.108477.
Epub ahead of print. PMID: 37330113.

3: Hopper AK, Zhang J. Captured: the elusive eukaryotic tRNA splicing enzyme.
Nat Struct Mol Biol. 2023 Jun;30(6):711-713. doi: 10.1038/s41594-023-00995-9.
PMID: 37231155.

4: Sutton MS, Pletnev S, Callahan V, Ko S, Tsybovsky Y, Bylund T, Casner RG,
Cerutti G, Gardner CL, Guirguis V, Verardi R, Zhang B, Ambrozak D, Beddall M,
Lei H, Yang ES, Liu T, Henry AR, Rawi R, Schön A, Schramm CA, Shen CH, Shi W,
Stephens T, Yang Y, Florez MB, Ledgerwood JE, Burke CW, Shapiro L, Fox JM, Kwong
PD, Roederer M. Vaccine elicitation and structural basis for antibody protection
against alphaviruses. Cell. 2023 Jun 8;186(12):2672-2689.e25. doi:
10.1016/j.cell.2023.05.019. Epub 2023 Jun 8. PMID: 37295404.

5: Negi H, Osei-Amponsa V, Ibrahim B, Evans CN, Sullenberger C, Loncarek J,
Chari R, Walters KJ. An engineered cell line with a hRpn1-attached handle to
isolate proteasomes. J Biol Chem. 2023 Jun 22:104948. doi:
10.1016/j.jbc.2023.104948. Epub ahead of print. PMID: 37354974.

6: Percze K, Tolnai ZJ, Eleveld M, Ou L, Du H, Olia AS, Kwong PD, de Jonge MI,
Mészáros T. Tryptophan-like side chain holding aptamers inhibit respiratory
syncytial virus infection of lung epithelial cells. Sci Rep. 2023 Jun
9;13(1):9403. doi: 10.1038/s41598-023-36428-2. PMID: 37296186; PMCID:
PMC10251311.

7: Yang M, Olatunji FP, Rhodes C, Balaratnam S, Dunne-Dombrink K, Seshadri S,
Liang X, Jones CP, Le Grice SFJ, Ferré-D'Amaré AR, Schneekloth JS Jr. Discovery
of Small Molecules Targeting the Frameshifting Element RNA in SARS-CoV-2 Viral
Genome. ACS Med Chem Lett. 2023 May 11;14(6):757-765. doi:
10.1021/acsmedchemlett.3c00051. PMID: 37312842; PMCID: PMC10258829.

8: Guan R, Lian T, Zhou BR, Wheeler D, Bai Y. Structural mechanism of LIN28B
nucleosome targeting by OCT4. Mol Cell. 2023 Jun 15;83(12):1970-1982.e6. doi:
10.1016/j.molcel.2023.05.030. PMID: 37327775; PMCID: PMC10276192.

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"

ARCHIVE: X-ray Crystallography, Cryo-Electron Microscopy, Integrative Structure Determination.
DISCUSSIONS - Name Change of the X-ray Diffraction SIG

F. Dyda, X. Ji: Considering rapid advancement of structural biology methods, we are proposing a change of the SIG name from "X-ray Diffraction" to "Structural Biology Methods," specifying that the SIG is mainly focused on methods in structural biology. Doing so, our SIG would be listed immediately after the "Structural Biology Interest Group" in the list of NIH SIGs. Please advise with your suggestions.

ARCHIVE: X-ray Crystallography, 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, X-ray Diffraction, 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