Newsletter 512 (April 15, 2024) NIH X-ray Diffraction SIG

MARCH 2024 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Lu X, Chandravanshi M, Sabbasani VR, Gaikwad S, Hughitt VK, Gyabaah-Kessie N, Scroggins BT, Das S, Myint W, Clapp ME, Schwieters CD, Dyba MA, Bolhuis DL, Koscielniak JW, Andresson T, Emanuele MJ, Brown NG, Matsuo H, Chari R, Citrin DE, Mock BA, Swenson RE, Walters KJ. 

A structure-based designed small molecule depletes hRpn13^Pru and a select group of KEN box proteins.

Nat Commun. 2024 Mar 20;15(1):2485. doi: 10.1038/s41467-024-46644-7. PMID: 38509117; PMCID: PMC10954691.

2: Dyda F, Hickman AB. 

A retrotransposon for site-specific gene transfer. 

Nat Biotechnol. 2024 Mar 18. doi: 10.1038/s41587-024-02180-9. Epub ahead of print. PMID: 38499759.

3: Torricella F, Tugarinov V, Clore GM. 

Nucleation of Huntingtin Aggregation Proceeds via Conformational Conversion of Pre-Formed, Sparsely-Populated Tetramers. 

Adv Sci (Weinh). 2024 Mar 12:e2309217. doi: 10.1002/advs.202309217. Epub ahead of print. PMID: 38476051.

4: Johnson S, Deme JC, Furlong EJ, Caesar JJE, Chevance FFV, Hughes KT, Lea SM.

Structural basis of directional switching by the bacterial flagellum. 

Nat Microbiol. 2024 Mar 8. doi: 10.1038/s41564-024-01630-z. Epub ahead of print. PMID: 38459206.

5: Park JE, Kim TS, Zeng Y, Mikolaj M, Il Ahn J, Alam MS, Monnie CM, Shi V, Zhou M, Chun TW, Maldarelli F, Narayan K, Ahn J, Ashwell JD, Strebel K, Lee KS.

Centrosome amplification and aneuploidy driven by the HIV-1-induced Vpr•VprBP•Plk4 complex in CD4⁺ T cells. 

Nat Commun. 2024 Mar 5;15(1):2017. doi: 10.1038/s41467-024-46306-8. PMID: 38443376; PMCID: PMC10914751.

6: Lederhofer J, Tsybovsky Y, Nguyen L, Raab JE, Creanga A, Stephens T, Gillespie RA, Syeda HZ, Fisher BE, Skertic M, Yap C, Schaub AJ, Rawi R, Kwong PD, Graham BS, McDermott AB, Andrews SF, King NP, Kanekiyo M. 

Protective human monoclonal antibodies target conserved sites of vulnerability on the underside of influenza virus neuraminidase. 

Immunity. 2024 Mar 12;57(3):574-586.e7. doi: 10.1016/j.immuni.2024.02.003. Epub 2024 Mar 1. PMID: 38430907; PMCID: PMC10962683.

7: Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH. 

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction. 

J Immunol. 2024 Mar 8:ji2300839. doi: 10.4049/jimmunol.2300839. Epub ahead of print. PMID: 38456672.

8: MacDonald ME, Wells NGM, Hassan BA, Dudley JA, Walters KJ, Korzhnev DM, Aramini JM, Smith CA. 

Effects of Xylanase A double mutation on substrate specificity and structural dynamics. 

J Struct Biol. 2024 Mar 2;216(2):108082. doi: 10.1016/j.jsb.2024.108082. Epub ahead of print. PMID: 38438058.

9: Muli CS, Tarasov SG, Walters KJ. 

High-throughput assay exploiting disorder-to-order conformational switches: application to the proteasomal Rpn10:E6AP complex. 

Chem Sci. 2024 Feb 6;15(11):4041-4053. doi: 10.1039/d3sc06370d. PMID: 38487241; PMCID: PMC10935766.

10: Bu W, Kumar A, Board NL, Kim J, Dowdell K, Zhang S, Lei Y, Hostal A, Krogmann T, Wang Y, Pittaluga S, Marcotrigiano J, Cohen JI. 

Epstein-Barr virus gp42 antibodies reveal sites of vulnerability for receptor binding and fusion to B cells. 

Immunity. 2024 Mar 12;57(3):559-573.e6. doi: 10.1016/j.immuni.2024.02.008. PMID: 38479361.

11: Lauber F, Deme JC, Liu X, Kjær A, Miller HL, Alcock F, Lea SM, Berks BC.

Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon. 

Nat Microbiol. 2024 Mar 27. doi: 10.1038/s41564-024-01644-7. Epub ahead of print. PMID: 38538833.

For timely listing, please send a heads-up E-mail to the Editor upon publication.

METHODS – Integrative Structural Biology

M. Bochtler, “X-rays, electrons, and neutrons as probes of atomic matter” PMID: 38412856.

METHODS – XFEL, 3D-printed liquid sheet jet technology

M. Trebbin, “Thinner than a knife’s edge: 3D-printed liquid sheet jet technology for solution phase XFEL experiments” PMID: 37910141.

METHODS – Cryo-EM, in Rational Design of Hybrid Inhibitors

B. Greber et al., “High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design” PMID: 38480681

G.J. Kleywegt, “Community recommendations on cryoEM data archiving and validation” PMID: 38358351.

M. Kschonsak et al., “Cryo-EM reveals an unprecedented binding site for Nav1.7 inhibitors enabling rational design of potent hybrid inhibitors” PMID: 36975198.

READINGS & TUTORIALS – Macromolecular Crystallography

D.J. Haas, “Fifty years on: why macromolecular cryocrystallography has been so successful” IUCr Newsletter (2023) 31(3).

W.A. Hendrickson, “Facing the phase problem” PMID: 37668214.

DATABASES – Structural Biology

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