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Newsletter No. 490
 May 15, 2023

ACA News, IUCr Newsletter, IUCr Meetings List

APRIL 2023 PUBLICATIONS BY MEMBERS OF THE GROUP 


1: Buel GR, Chen X, Kayode O, Cruz A, Walters KJ. <sup>1</sup>H, <sup>15</sup>N,
<sup>13</sup>C backbone and Cβ resonance assignments for UBQLN1 UBA and UBAA
domains. Biomol NMR Assign. 2023 Apr 6. doi: 10.1007/s12104-023-10127-5. Epub
ahead of print. PMID: 37022617.

2: Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K,
Yang W. Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature.
2023 Apr 19. doi: 10.1038/s41586-023-05959-z. Epub ahead of print. PMID:
37076618.

3: Nim YS, Fong IYH, Deme J, Tsang KL, Caesar J, Johnson S, Pang LTH, Yuen NMH,
Ng TLC, Choi T, Wong YYH, Lea SM, Wong KB. Delivering a toxic metal to the
active site of urease. Sci Adv. 2023 Apr 21;9(16):eadf7790. doi:
10.1126/sciadv.adf7790. Epub 2023 Apr 21. PMID: 37083535; PMCID: PMC10121161.

4: Tugarinov V, Baber JL, Clore GM. A methyl-TROSY based <sup>13</sup>C
relaxation dispersion NMR experiment for studies of chemical exchange in
proteins. J Biomol NMR. 2023 Apr 25. doi: 10.1007/s10858-023-00413-8. Epub ahead
of print. PMID: 37095392.

5: Wilson BAP, Li N, Martinez Fiesco JA, Dalilian M, Wang D, Smith EA, Wamiru A,
Shah R, Goncharova EI, Beutler JA, Grkovic T, Zhang P, O'Keefe BR. Biochemical
Discovery, Intracellular Evaluation, and Crystallographic Characterization of
Synthetic and Natural Product Adenosine 3',5'-Cyclic Monophosphate-Dependent
Protein Kinase A (PKA) Inhibitors. ACS Pharmacol Transl Sci. 2023 Mar
21;6(4):633-650. doi: 10.1021/acsptsci.3c00010. PMID: 37082750; PMCID:
PMC10111623.

6: Andrews SF, Cominsky LY, Shimberg GD, Gillespie RA, Gorman J, Raab JE, Brand
J, Creanga A, Gajjala SR, Narpala S, Cheung CSF, Harris DR, Zhou T, Gordon I,
Holman L, Mendoza F, Houser KV, Chen GL, Mascola JR, Graham BS, Kwong PD, Widge
A, Dropulic LK, Ledgerwood JE, Kanekiyo M, McDermott AB. An influenza H1
hemagglutinin stem-only immunogen elicits a broadly cross-reactive B cell
response in humans. Sci Transl Med. 2023 Apr 19;15(692):eade4976. doi:
10.1126/scitranslmed.ade4976. Epub 2023 Apr 19. PMID: 37075126.

7: Sastry M, Changela A, Gorman J, Xu K, Chuang GY, Shen CH, Cheng C, Geng H,
O'Dell S, Ou L, Rawi R, Reveiz M, Stewart-Jones GBE, Wang S, Zhang B, Zhou T,
Biju A, Chambers M, Chen X, Corrigan AR, Lin BC, Louder MK, McKee K, Nazzari AF,
Olia AS, Parchment DK, Sarfo EK, Stephens T, Stuckey J, Tsybovsky Y, Verardi R,
Wang Y, Zheng CY, Chen Y, Doria-Rose NA, McDermott AB, Mascola JR, Kwong PD.
Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion
Peptide and Variation in Peptide Length to Improve HIV Neutralization. J Virol.
2023 Apr 26:e0160422. doi: 10.1128/jvi.01604-22. Epub ahead of print. PMID:
37098956.

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 - 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