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Newsletter No. 498
September 18, 2023

ACA News, IUCr Newsletter, IUCr Meetings List


AUGUST 2023 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Mayo KR, Basford MA, Carroll RJ, Dillon M, Fullen H, Leung J, Master H, Rura
S, Sulieman L, Kennedy N, Banks E, Bernick D, Gauchan A, Lichtenstein L, Mapes
BM, Marginean K, Nyemba SL, Ramirez A, Rotundo C, Wolfe K, Xia W, Azuine RE,
Cronin RM, Denny JC, Kho A, Lunt C, Malin B, Natarajan K, Wilkins CH, Xu H,
Hripcsak G, Roden DM, Philippakis AA, Glazer D, Harris PA. The <i>All of Us</i>
Data and Research Center: Creating a Secure, Scalable, and Sustainable Ecosystem
for Biomedical Research
. Annu Rev Biomed Data Sci. 2023 Aug 10;6:443-464. doi:
10.1146/annurev-biodatasci-122120-104825. PMID: 37561600.

2: Mayer ML, Nicoll RA. Jeffrey Watkins (1929-2023). Neuron. 2023 Aug
2;111(15):2280-2281. doi: 10.1016/j.neuron.2023.07.004. PMID: 37536288.

3: Hayne CK, Sekulovski S, Hurtig JE, Stanley RE, Trowitzsch S, van Hoof A. New
Insights into RNA processing by the eukaryotic tRNA Splicing Endonuclease
. J
Biol Chem. 2023 Aug 4:105138. doi: 10.1016/j.jbc.2023.105138. Epub ahead of
print. PMID: 37544645.

4: Ding J, Deme JC, Stagno JR, Yu P,
Lea SM, Wang YX. Capturing heterogeneous
conformers of cobalamin riboswitch by cryo-EM
. Nucleic Acids Res. 2023 Aug
3:gkad651. doi: 10.1093/nar/gkad651. Epub ahead of print. PMID: 37534568.

5: Metcalfe RD, Martinez Fiesco JA, Bonet-Ponce L, Kluss JH, Cookson MR,
Zhang P. Structure and regulation of full-length human leucine-rich repeat kinase 1.
Nat Commun. 2023 Aug 9;14(1):4797. doi: 10.1038/s41467-023-40532-2. PMID:
37558661; PMCID: PMC10412621.

6: Olia AS, Cheng C, Zhou T, Biju A, Harris DR, Changela A, Duan H, Ivleva VB,
Kong WP, Ou L, Rawi R, Tsybovsky Y, Van Wazer DJ, Corrigan AR, Gonelli CA, Lee
M, McKee K, Narpala S, O'Dell S, Parchment DK, Stancofski ED, Stephens T, Tan I,
Teng IT, Wang S, Wei Q, Yang Y, Yang Z, Zhang B; VRC Production Program; Novak
J, Renfrow MB, Doria-Rose NA, Koup RA, McDermott AB, Gall JG, Lei QP, Mascola
JR,
Kwong PD. Soluble prefusion-closed HIV-envelope trimers with glycan-covered
bases
. iScience. 2023 Jul 15;26(8):107403. doi: 10.1016/j.isci.2023.107403.
PMID: 37554450; PMCID: PMC10404741.

7: Wojtaszek JL, Hoff KE, Longley MJ, Kaur P, Andres SN, Wang H, Williams RS,
Copeland WC. Structure-specific roles for PolG2-DNA complexes in maintenance and
replication of mitochondrial DNA
. Nucleic Acids Res. 2023 Aug 18:gkad679. doi:
10.1093/nar/gkad679. Epub ahead of print. PMID: 37592734.

8: Menin L, Weber J, Villa S, Martini E, Maspero E, Niño CA, Cancila V, Poli A,
Maiuri P, Palamidessi A, Frittoli E, Bianchi F, Tripodo C,
Walters KJ, Giavazzi
F, Scita G, Polo S. A planar polarized MYO6-DOCK7-RAC1 axis promotes tissue
fluidification in mammary epithelia
. Cell Rep. 2023 Aug 29;42(8):113001. doi:
10.1016/j.celrep.2023.113001. Epub 2023 Aug 16. PMID: 37590133.

9: Park JE, Kirsch K, Lee H, Oliva P, Ahn JI, Ravishankar H, Zeng Y, Fox SD,
Kirby SA, Badhwar P, Andresson T, Jacobson KA, Lee KS. Specific inhibition of an
anticancer target, polo-like kinase 1, by allosterically dismantling its
mechanism of substrate recognition
. Proc Natl Acad Sci U S A. 2023 Aug
29;120(35):e2305037120. doi: 10.1073/pnas.2305037120. Epub 2023 Aug 21. PMID:
37603740.

10: Liu C, Wang L, Merriam JS, Shi W, Yang ES, Zhang Y, Chen M, Kong WP, Cheng
C, Tsybovsky Y, Stephens T, Verardi R, Leung K, Stein C, Olia AS, Harris DR,
Choe M, Zhang B, Graham BS,
Kwong PD, Koup RA, Pegu A, Mascola JR. Self-
assembling SARS-CoV-2 spike-HBsAg nanoparticles elicit potent and durable
neutralizing antibody responses via genetic delivery
. NPJ Vaccines. 2023 Aug
8;8(1):111. doi: 10.1038/s41541-023-00707-w. PMID: 37553406; PMCID: PMC10409857.

11: Glögl M, Friedrich N, Cerutti G, Lemmin T, Kwon YD, Gorman J, Maliqi L,
Mittl PRE, Hesselman MC, Schmidt D, Weber J, Foulkes C, Dingens AS, Bylund T,
Olia AS, Verardi R, Reinberg T, Baumann NS, Rusert P, Dreier B, Shapiro L,
Kwong PD, Plückthun A, Trkola A. Trapping the HIV-1 V3 loop in a helical conformation
enables broad neutralization
. Nat Struct Mol Biol. 2023 Aug 21. doi:
10.1038/s41594-023-01062-z. Epub ahead of print. PMID: 37605043.

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 CrystallographyCryo-Electron MicroscopyIntegrative 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 The Future of Structural Biology

T. Terwiliger, "AlphaFold changes everything (and nothing)" (2022)

O. Carugo and K. Djinovic-Carugo, "Structural biology: A golden era" (2023)

R.J. Read et al., "AlphaFold and the future of structural biology" (2023)


ARCHIVE: CrystallographyX-ray DiffractionStructural BiologyStructure Prediction

 LINKS Suggestions?

Databases: 
AlphaFold DB, BioCyc, DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe, 
                  PDB SARS-CoV-2 Resources
SARS-CoV-2 Related StructuresRaMP-DB,
                  virusMED,


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


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

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