To:                                                                                X-Ray NIH

Subject: Newsletter 508 (February 19, 2024) NIH X-ray Diffraction SIG

 

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JANUARY 2024 PUBLICATIONS BY MEMBERS OF THE GROUP

 

1: Zhang J.

Recognition of the tRNA structure: Everything everywhere but not all at once.

Cell Chem Biol. 2024 Jan 18;31(1):36-52.

doi: 10.1016/j.chembiol.2023.12.008. Epub 2023 Dec 29. PMID: 38159570.

 

2: Gorman J, Cheung CS, Duan Z, Ou L, Wang M, Chen X, Cheng C, Biju A, Sun Y, Wang P, Yang Y, Zhang B, Boyington JC, Bylund T, Charaf S, Chen SJ, Du H, Henry AR, Liu T, Sarfo EK, Schramm CA, Shen CH, Stephens T, Teng IT, Todd JP, Tsybovsky Y, Verardi R, Wang D, Wang S, Wang Z, Zheng CY, Zhou T, Douek DC, Mascola JR, Ho DD, Ho M, Kwong PD.

Cleavage-intermediate Lassa virus trimer elicits neutralizing responses, identifies neutralizing nanobodies, and reveals an apex-situated site-of-vulnerability.

Nat Commun. 2024 Jan 4;15(1):285.

doi: 10.1038/s41467-023-44534-y. PMID: 38177144; PMCID: PMC10767048.

 

3: Accogli A, Shakya S, Yang T, Insinna C, Kim SY, Bell D, Butov KR, Severino M, Niceta M, Scala M, Lee HS, Yoo T, Stauffer J, Zhao H, Fiorillo C, Pedemonte M, Diana MC, Baldassari S, Zakharova V, Shcherbina A, Rodina Y, Fagerberg C, Roos LS, Wierzba J, Dobosz A, Gerard A, Potocki L, Rosenfeld JA, Lalani SR, Scott TM, Scott D, Azamian MS, Louie R, Moore HW, Champaigne NL, Hollingsworth G, Torella A, Nigro V, Ploski R, Salpietro V, Zara F, Pizzi S, Chillemi G, Ognibene M, Cooney E, Do J, Linnemann A, Larsen MJ, Specht S, Walters KJ, Choi HJ, Choi M, Tartaglia M, Youkharibache P, Chae JH, Capra V, Park SG, Westlake CJ.

Variants in the WDR44 WD40-repeat domain cause a spectrum of ciliopathy by impairing ciliogenesis initiation.

Nat Commun. 2024 Jan 8;15(1):365.

doi: 10.1038/s41467-023-44611-2. PMID: 38191484; PMCID: PMC10774338.

 

4: Pegu A, Lovelace SE, DeMouth ME, Cully MD, Morris DJ, Li Y, Wang K, Schmidt SD, Choe M, Liu C, Chen X, Viox E, Rowshan A, Taft JD, Zhang B, Xu K, Duan H, Ou L, Todd JP, Kong R, Li H, Shaw GM, Doria-Rose NA, Kwong PD, Koup RA, Mascola JR.

Antibodies targeting the fusion peptide on the HIV envelope provide protection to rhesus macaques against mucosal SHIV challenge.

Sci Transl Med. 2024 Jan 17;16(730):eadh9039.

doi: 10.1126/scitranslmed.adh9039. Epub 2024 Jan 17. PMID: 38232141.

 

5: Lian T, Guan R, Zhou BR, Bai Y,.

Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα.

Nat Struct Mol Biol. 2024 Jan 24.

doi: 10.1038/s41594-023-01189-z. Epub ahead of print. PMID: 38267599.

 

6: Casiano Matos J, Harichandran K, Tang J, Sviridov DO, Sidoti Migliore G, Suzuki M, Olano LR, Hobbs A, Kumar A, Paskel MU, Bonsignori M, Dearborn AD, Remaley AT, Marcotrigiano J.

Hepatitis C virus E1 recruits high-density lipoprotein to support infectivity and evade antibody recognition.

J Virol. 2024 Jan 23;98(1):e0084923.

doi: 10.1128/jvi.00849-23. Epub 2024 Jan 4. PMID: 38174935; PMCID: PMC10804985.

 

7: Oda K, Wlodawer A.

Development of Enzyme-Based Approaches for Recycling PET on an Industrial Scale.

Biochemistry. 2024 Jan 29.

doi: 10.1021/acs.biochem.3c00554. Epub ahead of print. PMID: 38285602.

 

8: Ao Y, Grover JR, Gifford L, Han Y, Zhong G, Katte R, Li W, Bhattacharjee R, Zhang B, Sauve S, Qin W, Ghimire D, Haque MA, Arthos J, Moradi M, Mothes W, Lemke EA, Kwong PD, Melikyan GB, Lu M.

Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging.

Cell Chem Biol. 2024 Jan 8:S2451-9456(23)00474-9.

doi: 10.1016/j.chembiol.2023.12.017. Epub ahead of print. PMID: 38232732.

 

9: Gridley J, Holland B, Salinas E, Trivedi S, Dravid P, Elrod E, Jin F, Kumari A, Batista MN, Thapa M, Rice CM, Marcotrigiano J, Kapoor A, Grakoui A.

Concerted synergy between viral-specific IgG and CD8+ T cells is critical for clearance of an HCV-related rodent hepacivirus.

Hepatology. 2024 Jan 12.

doi: 10.1097/HEP.0000000000000753. Epub ahead of print. PMID: 38214558.

 

10: Prabhakaran M, Matassoli F, Leggat D, Hoover A, Srikanth A, Wu W, Henry AR, Wang J, Lin BC, Teng IT, Schramm CA, Castro M, Serebryannyy L, Jean-Baptiste N, Moore C, Gajjala S, Todd JM, McCarthy E, Narpala S, Francica J, Program VP, Corbett-Helaire KS, Douek DC, Kwong PD, Seder RA, Andrews SF, McDermott AB.

Adjuvanted SARS-CoV-2 spike protein vaccination elicits long-lived plasma cells in nonhuman primates.

Sci Transl Med. 2024 Jan 3;16(728):eadd5960.

doi: 10.1126/scitranslmed.add5960. Epub 2024 Jan 3. PMID: 38170789.

 

11: Levdansky Y, Valkov E.

Reconstitution of Human CCR4-NOT Complex from Purified Proteins and an Assay of Its Deadenylation Activity.

Methods Mol Biol. 2024;2723:1-17.

doi: 10.1007/978-1-0716-3481-3_1. PMID: 37824061.

 

12: Hayne CK, Butay KJU, Stewart ZD, Krahn JM, Perera L, Williams JG, Petrovitch RM, Deterding LJ, Matera AG, Borgnia MJ, Stanley RE.

Author Correction: Structural basis for pre-tRNA recognition and processing by the human Trna splicing endonuclease complex.

Nat Struct Mol Biol. 2024 Jan 9.

doi: 10.1038/s41594-024-01213-w. Epub ahead of print. Erratum for: Nat Struct Mol Biol. 2023 Jun;30(6):824-833. PMID: 38196035.

 

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

 

 

METHODS – Cryo-EM, Data Archiving and Validation

 

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

 

 

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

 

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,

 

Xinhua Ji, Ph.D.

Senior Investigator

National Cancer Institute, NIH

Phone: (301) 846-5035