Newsletter 531 (May 19, 2025) NIH Structural Biology Methods SIG

APRIL 2025 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Lu X, Sabbasani VR, Hassan B, Swenson RE, Walters KJ. 

Optimization of the PROTAC linker region of the proteasome substrate receptor hRpn13 rationalized structural modeling with molecular dynamics. 

J Biol Chem. 2025 Apr 18:108520. doi: 10.1016/j.jbc.2025.108520. Epub ahead of print. 

PMID: 40254254.

2: Chen L, Dickerhoff J, Zheng KW, Erramilli S, Feng H, Wu G, Onel B, Chen Y, Wang KB, Carver M, Lin C, Sakai S, Wan J, Vinson C, Hurley L, Kossiakoff AA, Deng N, Bai Y, Noinaj N, Yang D. 

Structural basis for nucleolin recognition of MYC promoter G-quadruplex.

Science. 2025 Apr 18;388(6744):eadr1752. doi: 10.1126/science.adr1752. Epub 2025 Apr 18. 

PMID: 40245140.

3: Tumbale PP, Jurkiw TJ, Krahn JM, Bokil NV, Admiraal SJ, Pedersen LC, Williams JS, Kunkel TA, O'Brien PJ, Williams RS. 

Molecular basis for RNA discrimination by human DNA ligase 1. 

Nucleic Acids Res. 2025 Apr 10;53(7):gkaf299. doi: 10.1093/nar/gkaf299. 

PMID: 40239996; PMCID: PMC12000876.

4: Rimkute I, Olia AS, Suleiman M, Woods KD, Bylund T, Morano NC, Tully ES, Verardi R, Bao S, Beddall MH, Chaimongkol N, Donaldson MM, Du R, Dulan CNM, Gorman J, Henry AR, Schramm CA, Sosnovtsev SV, Stephens T, Todd JP, Tsybovsky Y, Douek DC, Green KY, Rawi R, Shapiro L, Zhou T, Kwong PD, Roederer M. 

A broadly protective human antibody for GI genogroup noroviruses. 

Nat Microbiol. 2025 Apr 10. doi: 10.1038/s41564-025-01952-6. Epub ahead of print. 

PMID: 40211068.

5: Jones CP, Ferré-D'Amaré AR. 

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus-programmed ribosomal frameshifting element. 

Proc Natl Acad Sci U S A. 2025 Apr 8;122(14):e2418418122. doi: 10.1073/pnas.2418418122. Epub 2025 Apr 2. 

PMID: 40172966; PMCID: PMC12002268.

MARCH 2025 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Jiang C, Li Z, Seok S, Li P, Ma Y, Podguski SK, Moturi S, Yoneda N, Kawai K, Uehara S, Ohnishi Y, Suemizu H, Zhang J, Cao H. 

Systemic Identification of Functionally Conserved Long Noncoding RNA Metabolic Regulators in Human and Mouse Livers. 

Gastroenterology. 2025 Mar 22:S0016-5085(25)00536-0. doi: 10.1053/j.gastro.2025.03.015. Epub ahead of print. 

PMID: 40127783.

2: Hu L, Wainman A, Andreeva A, Apizi M, Alvarez-Rodrigo I, Wong SS, Saurya S, Sheppard D, Cottee M, Johnson S, Lea SM, Raff JW, van Breugel M, Feng Z. 

The conserved Spd-2/CEP192 domain adopts a unique protein fold to promote centrosome scaffold assembly. 

Sci Adv. 2025 Mar 21;11(12):eadr5744. doi: 10.1126/sciadv.adr5744. Epub 2025 Mar 19. 

PMID: 40106572; PMCID: PMC11922060.

3: Hedger AK, Myint W, Lee JM, Suchenski Loustaunau D, Balachandran V, Shaqra AM, Kurt Yilmaz N, Watts JK, Matsuo H, Schiffer CA. 

Next generation APOBEC3 inhibitors: optimally designed for potency and nuclease stability. 

Nucleic Acids Res. 2025 Mar 20;53(6):gkaf234. doi: 10.1093/nar/gkaf234. 

PMID: 40156866; PMCID: PMC11954526.

4: Soubias O, Foley SL, Jian X, Jackson RA, Zhang Y, Rosenberg EM Jr, Li J, Heinrich F, Johnson ME, Sodt AJ, Randazzo PA, Byrd RA. 

The PH domain in the ArfGAP ASAP1 drives catalytic activation through an unprecedented allosteric mechanism. 

Res Sq [Preprint]. 2025 Mar 19:rs.3.rs-5462793. doi: 10.21203/rs.3.rs-5462793/v1. 

PMID: 40166026; PMCID: PMC11957191.

5: Mondal T, Song J, Banerjee A. 

In vitro reconstitution reveals substrate selectivity of protein S-acyltransferases. 

J Biol Chem. 2025 Mar 14;301(4):108406. doi: 10.1016/j.jbc.2025.108406. Epub ahead of print. 

PMID: 40090582; PMCID: PMC12018989.

6: Mantus GE, Cerutti G, Chambers M, Gillespie RA, Shimberg GD, Spangler A, Gorman J, Zhou T, Shen CH, Kanekiyo M, Kwong PD, Shapiro L, Andrews SF. 

Distinct binding modes drive the broad neutralization profile of two persistent influenza hemagglutinin stem-specific antibody lineages. 

Structure. 2025 Mar 11:S0969-2126(25)00063-2. doi: 10.1016/j.str.2025.02.010. Epub ahead of print.

PMID: 40112805.

7: Mariano G, Deme JC, Readshaw JJ, Grobbelaar MJ, Keenan M, El-Masri Y, Bamford L, Songra S, Blower TR, Palmer T, Lea SM. 

Modularity of Zorya defense systems during phage inhibition. 

Nat Commun. 2025 Mar 8;16(1):2344. doi: 10.1038/s41467-025-57397-2. 

PMID: 40057510; PMCID: PMC11890865.

8: Bou-Nader C, Link KA, Suddala KC, Knutson JR, Zhang J. 

Structures of complete HIV-1 TAR RNA portray a dynamic platform poised for protein binding and structural remodeling. 

Nat Commun. 2025 Mar 6;16(1):2252. doi: 10.1038/s41467-025-57519-w. 

PMID: 40050622; PMCID: PMC11885821.

9: De Pace R, Bonifacino JS, Ghosh S. 

Puromycin Proximity Ligation Assay (Puro- PLA) to Assess Local Translation in Axons From Human Neurons. 

Bio Protoc. 2025 Mar 5;15(5):e5224. doi: 10.21769/BioProtoc.5224. 

PMID: 40084072; PMCID: PMC11896778.

10: Park J, Lindesmith LC, Olia AS, Costantini VP, Brewer-Jensen PD, Mallory ML, Kelley CE, Satterwhite E, Longo V, Tsybovsky Y, Stephens T, Marchioni J, Martins CA, Huang Y, Chaudhary R, Zweigart M, May SR, Reyes Y, Flitter B, Vinjé J, Tucker SN, Ippolito GC, Lavinder JJ, Snijder J, Kwong PD, Georgiou G, Baric RS.

Broadly neutralizing antibodies targeting pandemic GII.4 variants or seven GII genotypes of human norovirus. 

Sci Transl Med. 2025 Mar 5;17(788):eads8214. doi: 10.1126/scitranslmed.ads8214. Epub 2025 Mar 5. 

Erratum in: Sci Transl Med. 2025  Apr 23;17(795):eadx9947. doi: 10.1126/scitranslmed.adx9947. 

PMID: 40043137.

11: Zhou BR, Orris B, Guan R, Lian T, Bai Y. 

Structural insights into the recognition of native nucleosomes by pioneer transcription factors.

Curr Opin Struct Biol. 2025 Mar 1;92:103024. doi: 10.1016/j.sbi.2025.103024. Epub ahead of print. 

PMID: 40024204.

FEBRUARY 2025 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Dauter Z, Jaskolski M. 

Honeycombs - their variety, topology and symmetry.

Acta Crystallogr A Found Adv. 2025 Mar 1;81(Pt 2):159-166. doi: 10.1107/S2053273325000889. Epub 2025 Feb 14. 

PMID: 39950307; PMCID: PMC11873813.

2: Ng MY, Wang H, Zhang H, Prucker I, Perera L, Goncharova E, Wamiru A, Jessen HJ, Stanley RE, Shears SB, Luo J, O'Keefe BR, Wilson BAP. 

Biochemical and biophysical characterization of inositol-tetrakisphosphate 1-kinase inhibitors.

J Biol Chem. 2025 Mar;301(3):108274. doi: 10.1016/j.jbc.2025.108274. Epub 2025 Feb 6. 

PMID: 39922495; PMCID: PMC11927698.

3: Stagno JR, Deme JC, Dwivedi V, Lee YT, Lee HK, Yu P, Chen SY, Fan L, Degenhardt MFS, Chari R, Young HA, Lea SM, Wang YX. 

Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells. 

Nucleic Acids Res. 2025 Feb 27;53(5):gkaf156. doi: 10.1093/nar/gkaf156. 

PMID: 40071935; PMCID: PMC11897892.

4: Naz Z, Rathore I, Saleem M, Rahman M, Wlodawer A, Rashid N.

A Bifunctional Phosphoglucomutase/Phosphomannomutase from Thermococcus kodakarensis Biophysical Analysis and Cryo-EM Structure. 

Biomolecules. 2025 Feb 21;15(3):319. doi: 10.3390/biom15030319. 

PMID: 40149855; PMCID: PMC11940775.

5: Joyce MG, Bu W, Chen WH, Gillespie RA, Andrews SF, Wheatley AK, Tsybovsky Y, Jensen JL, Stephens T, Prabhakaran M, Fisher BE, Narpala SR, Bagchi M, McDermott AB, Nabel GJ, Kwong PD, Mascola JR, Cohen JI, Kanekiyo M. 

Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350. 

Immunity. 2025 Feb 11;58(2):295-308.e5. doi: 10.1016/j.immuni.2025.01.010. Epub 2025 Feb 4. 

PMID: 39909035.

6: Fu ZQ, Geisbrecht BV, Bouyain S, Dyda F, Chrzas J, Kandavelu P, Miller DJ, Wang BC. 

I/σI vs {Rmerg, Rmeas, Rpim, CC1/2} for Crystal Diffraction Data Quality Evaluation. 

bioRxiv [Preprint]. 2025 Feb 2:2024.12.10.627855. doi: 10.1101/2024.12.10.627855.

PMID: 39713313; PMCID: PMC11661158.

7: Borgognoni KM, Stanley RE. 

How a ribosomal protein avoids mixed signals. 

Nat Cell Biol. 2025 Feb;27(2):182-183. doi: 10.1038/s41556-024-01606-5. 

PMID: 39890953.

JANUARY 2025 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Schafer JM, Muli CS, Heikal RA, Dyba MA, Tarasov SG, Stratton MM, Strieter ER, Walters KJ. 

Optimized isolation of enzymatically active ubiquitin E3 ligase E6AP/UBE3A from mammalian cells. 

Protein Expr Purif. 2025 Apr;228:106661. doi: 10.1016/j.pep.2025.106661. Epub 2025 Jan 9. 

PMID: 39798888; PMCID: PMC11779574.

2: Rubach P, Majorek KA, Gucwa M, Murzyn K, Wlodawer A, Minor W. 

Advances in cryo-electron microscopy (cryoEM) for structure-based drug discovery.

Expert Opin Drug Discov. 2025 Feb;20(2):163-176. doi:10.1080/17460441.2025.2450636. Epub 2025 Jan 16. 

PMID: 39789967.

3: Witt KC, Dziulko A, An J, Pekovic F, Cheng AX, Liu GY, Lee OV, Turner DJ, Lari A, Gaidt MM, Chavez R, Fattinger SA, Abraham P, Dhaliwal H, Lee AY, Kotov DI, Coscoy L, Glaunsinger BA, Valkov E, Chuong EB, Vance RE. 

The SP140-RESIST pathway regulates interferon mRNA stability and antiviral immunity. 

bioRxiv [Preprint]. 2025 Jan 29:2024.08.28.610186. doi: 10.1101/2024.08.28.610186.

PMID: 39974928; PMCID: PMC11838211.

4: Mason RD, Zhang B, Morano NC, Shen CH, McKee K, Heimann A, Du R, Nazzari AF, Hodges S, Kanai T, Lin BC, Louder MK, Doria-Rose NA, Zhou T, Shapiro L, Roederer M, Kwong PD, Gorman J. 

Structural development of the HIV-1 apex-directed PGT145-PGDM1400 antibody lineage. 

Cell Rep. 2025 Jan 28;44(1):115223. doi: 10.1016/j.celrep.2024.115223. Epub 2025 Jan 17. 

PMID: 39826122; PMCID: PMC11883830.

5: Gorman J, Du R, Lai YT, Ahmadi MS, King HAD, Song K, Manalang K, Gonelli CA, Schramm CA, Cheng C, Nguyen R, Ambrozak D, Druz A, Shen CH, Yang Y, Douek DC, Kwong PD, Roederer M, Mason RD. 

Isolation and structure of broad SIV- neutralizing antibodies reveal a proximal helical MPER epitope recognized by a rhesus multi-donor class. 

Cell Rep. 2025 Jan 28;44(1):115163. doi: 10.1016/j.celrep.2024.115163. Epub 2025 Jan 9. 

PMID: 39792559; PMCID: PMC11979902.

6: Das M, Hile SE, Brewster J, Boer JL, Bezalel-Buch R, Guo Q, Yang W, Burgers PM, Eckert KA, Freudenreich CH. 

DNA polymerase zeta can efficiently replicate structures formed by AT/TA repeat sequences and prevent their deletion. 

Nucleic Acids Res. 2025 Jan 24;53(3):gkae1254. doi: 10.1093/nar/gkae1254. 

PMID: 39727171; PMCID: PMC11797062.

7: Yang X, Chen X, Yang W, Pommier Y. 

Structural insights into human topoisomerase 3β DNA and RNA catalysis and nucleic acid gate dynamics. 

Nat Commun. 2025 Jan 19;16(1):834. doi: 10.1038/s41467-025-55959-y. 

PMID: 39828754; PMCID: PMC11743793.

8: Loughran G, De Pace R, Ding N, Zhang J, Jungreis I, Carancini G, Mudge JM, Wang J, Kellis M, Atkins JF, Baranov PV, Firth AE, Li X, Bonifacino JS, Khan YA.

Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active proteoform that supports myocardial function.

bioRxiv [Preprint]. 2025 Jan 14:2024.08.30.610563. doi: 10.1101/2024.08.30.610563.

PMID: 39372779; PMCID: PMC11451614.

9: Hickman AB, Lannes L, Furman CM, Hong C, Franklin L, Ghirlando R, Ghosh A, Luo W, Konstantinidou P, Lorenzi HA, Grove A, Haase AD, Wilson MH, Dyda F.

Activity of the mammalian DNA transposon piggyBat from Myotis lucifugus is restricted by its own transposon ends. 

Nat Commun. 2025 Jan 7;16(1):458. doi: 10.1038/s41467-024-55784-9. 

PMID: 39774116; PMCID: PMC11707139.

10: Wright ZM, Butay KJ, Krahn JM, Wilson IM, Gabel SA, DeRose EF, Hissein IS, Williams JG, Borgnia MJ, Frazier MN, Mueller GA, Stanley RE. 

Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates. 

Nat Commun. 2025 Jan 4;16(1):391. doi: 10.1038/s41467-024-55682-0. 

PMID: 39755678; PMCID: PMC11700208.

11: Qiu C, Crittenden SL, Carrick BH, Dillard LB, Costa Dos Santos SJ, Dandey VP, Dutcher RC, Viverette EG, Wine RN, Woodworth J, Campbell ZT, Wickens M, Borgnia MJ, Kimble J, Hall TMT. 

A higher order PUF complex is central to regulation of C. elegans germline stem cells. 

Nat Commun. 2025 Jan 2;16(1):123. doi: 10.1038/s41467-024-55526-x. 

PMID: 39747099; PMCID: PMC11696143.

12: Gupta R, Gaikwad S, Qui H, Bou-Nader C, Zhang J, Hinnebusch AG. 

Purification and Analysis of eIF2α Phosphorylation by Stress-Activated Protein Kinase Gcn2 from S. cerevisiae. 

Methods Mol Biol. 2025;2882:195-220. doi: 10.1007/978-1-0716-4284-9_10. 

PMID: 39992511.

13: Mantus GE, Chopde AJ, Gorman J, Cominsky LY, Ourahmane A, Creanga A, Shimberg GD, Gillespie RA, Van Wazer DJ, Zhou T, Gajjala SR, Williams C, Maestle E, Reed DS, Serebryannyy L, Costner P, Holman L, Casazza JP, Koup RA, Dropulic LK, Kwong PD, McDermott AB, Kanekiyo M, Andrews SF. 

Vaccination with different group 2 influenza subtypes alters epitope targeting and breadth of hemagglutinin stem-specific human B cells. 

Sci Transl Med. 2025 Jan;17(779):eadr8373. doi: 10.1126/scitranslmed.adr8373. Epub 2025 Jan 1. 

PMID: 39742506.

14: Naskręcki B, Malinowski J, Dauter Z, Jaskolski M. 

Growth functions of periodic space tessellations. 

Acta Crystallogr A Found Adv. 2025 Jan 1;81(Pt 1):64-81. doi: 10.1107/S2053273324010763. Epub 2025 Jan 1. 

PMID: 39635759; PMCID: PMC11694217.

15: Dyda F, Hickman AB. 

A retrotransposon for site-specific gene transfer. 

Nat Biotechnol. 2025 Jan;43(1):31-33. doi: 10.1038/s41587-024-02180-9. 

PMID: 38499759.

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

RECENT TOPICS IN THE LITERATURE:

METHODS – Sample Preparation Tips

Y. Huang et al., “Recent Advances in Expression Screening and Sample Evaluation for Structural Studies of Membrane Proteins” PMID: 39362625.

K. McGuire et al., “Tuning ice thickness using the chameleon for high-quality cryoEM data collection” PMID: 38746094.

B. Cook et al., “Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification” PMID: 39091810.

R. Warmack et al., “Anaerobic cryoEM protocols for air- sensitive nitrogenase proteins” PMID: 38575747.

I.J. Hirst et al., “CryoEM grid preparation: a closer look at advancements and impact of preparation mode and new approaches” PMID: 38864435.

S. Yadav and K.R. Vinothkumar, “Factors affecting macromolecule orientations in thin films formed in cryo-EM” PMID: 38935342.

S.E.J. Bowman et al., “Preparing research samples for safe arrival at centers and facilities: recipes for successful experiments” PMID: 38990054.

METHODS – Macromolecular Crystallography

M. Schaefer et al., “Surface-mutagenesis strategies to enable structural biology crystallization platforms”  PMID: 39207897.

METHODS – Integrative Structural Biology

M. Bazayeva et al., “A database overview of metal-coordination distances in metalloproteins” PMID: 38682667.

H. Zheng et al., “PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules” PMID: 38463967.

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 – Micro-ED, AlphaFold-Assisted

J.E. Miller et al., “AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography” PMID: 38451205.

METHODS – Cryo-EM

D. Bobe et al., “Multi-species cryoEM calibration and workflow verification standard” PMID: 39494502

C.L. Lawson et al., “Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge” PMID: 38343795.

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.

METHODS – SAXS

K. Lytje and J.S. Pederson, “Validation of electron-microscopy maps using solution small-angle X-ray scattering” PMID: 38935344.

METHODS – NMR and Ligand Screening

M. Bütikofer et al., “Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR” PMID: 38957136.

METHODS – AlphaFold

A.M. Lau et al., “Exploring structural diversity across the protein universe with The Encyclopedia of Domains” PMID: 39480926.

J. Abramson et al., “Accurate structure prediction of biomolecular interactions with AlphaFold 3” PMID: 38718835.

READINGS & TUTORIALS – General Structural Biology

L.C. Schofield et al., “Post-translational modifications in the Protein Data Bank” PMID: 39207896.

READINGS & TUTORIALS – Macromolecular Crystallography

K.L. Shelley and E.F. Garman, “Identifying and avoiding radiation damage in macromolecular crystallography” PMID: 38700059.

G. Khusainov et al., “The time revolution in macromolecular crystallography” PMID: 38616866.

J.R. Helliwell et al., “The evolution of raw data archiving and the growth of its importance in crystallography” PMID: 38864497.

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.

READINGS & TUTORIALS – Cryo-EM

G.C. Lander, “Single particle cryo-EM map and model validation: It's not crystal clear” PMID: 39293191.

E. Nogales & J. Mahamid, “Bridging structural and cell biology with cryo-electron microscopy” PMID: 38570716.

READINGS & TUTORIALS – Serial Crystallography

A. Henkel and D. Oberthur, “A snapshot love story: what serial crystallography has done for us” PMID: 38984902.

READINGS & TUTORIALS – MicroED

A. Haymaker & B.L. Nannenga, “Advances and applications of microcrystal electron diffraction (MicroED)” PMID: 10882645.

READINGS & TUTORIALS – AlphaFold/AI

E. Callaway, “Chemistry Nobel goes to developers of AlphaFold AI that predicts protein structures” PMID: 39384918.

E. Callaway, “The huge protein database that spawned AlphaFold and biology's AI revolution” PMID: 39424937.

S. Subramaniam, “Structural biology in the age of AI” PMID: 38066345.

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, 

UPCOMING MEETINGS, CONFERENCES, & WORKSHOPS

75^th ACA Annual Meeting, July 18-23, 2025

Lombard, IL

Microscopy Society of America Annual Meeting, July 27-31, 2025

Salt Lake City, UT

Cold Spring Harbor Laboratory Macromolecular Crystallography Course, October 12-28, 2025

Cold Spring Harbor, NY

Application Deadline: July 15, 2025