Jinwei Zhang, Ph.D.

Deputy Chief: Laboratory of Molecular Biology
Section Chief: Structural Biology of Noncoding RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology

Scientific Focus Areas: RNA Biology, Structural Biology, Molecular Biology and Biochemistry, Microbiology and Infectious Diseases, Biomedical Engineering and Biophysics

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Publications

A selection of recent and significant publications can be viewed below.

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Structural basis of MALAT1 RNA maturation and mascRNA biogenesis.: Skeparnias I, Bou-Nader C, Anastasakis DG, Fan L, Wang YX, Hafner M, Zhang J.; Nat Struct Mol Biol (2024 Nov) 31:1655-1668. Abstract/Full Text
Structural basis of NEAT1 lncRNA maturation and menRNA instability.: Skeparnias I, Zhang J.; Nat Struct Mol Biol (2024 Nov) 31:1650-1654. Abstract/Full Text
Structures of complete HIV-1 TAR RNA portray a dynamic platform poised for protein binding and structural remodeling.: Bou-Nader C, Link KA, Suddala KC, Knutson JR, Zhang J.; Nat Commun (2025 Mar 6) 16:2252. Abstract/Full Text
Structural basis of tRNA recognition by the widespread OB fold.: Umuhire Juru A, Ghirlando R, Zhang J.; Nat Commun (2024 Jul 29) 15:6385. Abstract/Full Text
The conformational space of RNase P RNA in solution.: Lee YT, Degenhardt MFS, Skeparnias I, Degenhardt HF, Bhandari YR, Yu P, Stagno JR, Fan L, Zhang J, Wang YX.; Nature (2025 Jan) 637:1244-1251. Abstract/Full Text

Additional Publications

Mitochondrial tRNA biogenesis, modifications and disease relevance.: Zhu WY, Skeparnias I, Shaukat AN, Zhang J, Liu RJ.; Nat Rev Mol Cell Biol (2026 Jul 24) Abstract/Full Text
Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.: Geng A, Roy R, Ken M, Li L, Chime A, Abou Assi H, Liu B, Bou-Nader C, Lee Y, Zhang J, Herschlag D, Goff SP, Al-Hashimi HM.; Cell (2026 May 14) 189:2934-2954.e25. Abstract/Full Text
Three-metal-ion catalysis by ribonuclease P holoenzyme: a new mechanistic insight into transfer RNA maturation.: Lee YT, Degenhardt MFS, Skeparnias I, Chen SY, Bhoge BA, Tarasov SG, Dyba MA, Shi D, Zhang J, Stagno JR, Wang YX.; Res Sq (2026 May 14) Abstract/Full Text
Structural basis for protein-free catalysis by ribonuclease P ribozyme.: Lee YT, Degenhardt MFS, Skeparnias I, Chen SY, Bhoge BA, Tarasov SG, Dyba MA, Zhang J, Stagno JR, Wang YX.; Nat Commun (2026 Apr 15) 17. Abstract/Full Text
Structural basis of double-stranded RNA recognition by the J2 monoclonal antibody.: Bou-Nader C, Juma KM, Bothra A, Brasington AJ, Ghirlando R, Suzuki M, Garboczi DN, Leppla SH, Zhang J.; Nat Commun (2025 Dec 13) 17:635. Abstract/Full Text
Specific targeting of transcriptional T-box riboswitches leads to effective inhibition of S. aureus.: Giarimoglou N, Kouvela A, Papakyriakou A, Zhang J, Stamatopoulou V, Stathopoulos C.; RNA (2025 Nov 17) 31:1749-1765. Abstract/Full Text
Determining structures of RNA conformers using AFM and deep neural networks.: Degenhardt MFS, Degenhardt HF, Bhandari YR, Lee YT, Ding J, Yu P, Heinz WF, Stagno JR, Schwieters CD, Watts NR, Wingfield PT, Rein A, Zhang J, Wang YX.; Nature (2025 Jan) 637:1234-1243. Abstract/Full Text
Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response.: Bou-Nader C, Gaikwad S, Bahmanjah S, Zhang F, Hinnebusch AG, Zhang J.; Proc Natl Acad Sci U S A (2024 Aug 27) 121:e2409628121. Abstract/Full Text
Recognition of the tRNA structure: Everything everywhere but not all at once.: Zhang J.; Cell Chem Biol (2024 Jan 18) 31:36-52. Abstract/Full Text
Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state.: Lee HK, Lee YT, Fan L, Wilt HM, Conrad CE, Yu P, Zhang J, Shi G, Ji X, Wang YX, Stagno JR.; Structure (2023 Jul 6) 31:848-859.e3. Abstract/Full Text
Determining structures of individual RNA conformers using atomic force microscopy images and deep neural networks.: Degenhardt MFS, Degenhardt HF, Bhandari YR, Lee YT, Ding J, Heinz WF, Stagno JR, Schwieters CD, Zhang J, Wang YX.; Res Sq (2023 Jun 7) Abstract/Full Text
Captured: the elusive eukaryotic tRNA splicing enzyme.: Hopper AK, Zhang J.; Nat Struct Mol Biol (2023 Jun) 30:711-713. Abstract/Full Text
Visualizing RNA conformational and architectural heterogeneity in solution.: Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno JR, Ma B, Nussinov R, Rein A, Zhang J, Wang YX.; Nat Commun (2023 Feb 9) 14:714. Abstract/Full Text
Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action.: Giarimoglou N, Kouvela A, Patsi I, Zhang J, Stamatopoulou V, Stathopoulos C.; Nucleic Acids Res (2022 Jun 10) 50:5834-5849. Abstract/Full Text
Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions.: Skeparnias I, Zhang J.; Noncoding RNA (2021 Dec 15) 7. Abstract/Full Text
Human cell based directed evolution of adenine base editors with improved efficiency.: Fu J, Li Q, Liu X, Tu T, Lv X, Yin X, Lv J, Song Z, Qu J, Zhang J, Li J, Gu F.; Nat Commun (2021 Oct 8) 12:5897. Abstract/Full Text
Interplay between Host tRNAs and HIV-1: A Structural Perspective.: Zhang J.; Viruses (2021 Sep 13) 13. Abstract/Full Text
HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization.: Bou-Nader C, Muecksch F, Brown JB, Gordon JM, York A, Peng C, Ghirlando R, Summers MF, Bieniasz PD, Zhang J.; Cell Host Microbe (2021 Sep 8) 29:1421-1436.e7. Abstract/Full Text
Improving RNA Crystal Diffraction Quality by Postcrystallization Treatment.: Zhang J, Ferré-D'Amaré AR.; Methods Mol Biol (2021) 2323:25-37. Abstract/Full Text
Unboxing the T-box riboswitches-A glimpse into multivalent and multimodal RNA-RNA interactions.: Zhang J.; Wiley Interdiscip Rev RNA (2020 Nov) 11:e1600. Abstract/Full Text
High-fidelity SaCas9 identified by directional screening in human cells.: Xie H, Ge X, Yang F, Wang B, Li S, Duan J, Lv X, Cheng C, Song Z, Liu C, Zhao J, Zhang Y, Wu J, Gao C, Zhang J, Gu F.; PLoS Biol (2020 Jul) 18:e3000747. Abstract/Full Text
Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions.: Bou-Nader C, Zhang J.; Molecules (2020 Jun 23) 25. Abstract/Full Text
An evolving tale of two interacting RNAs-themes and variations of the T-box riboswitch mechanism.: Suddala KC, Zhang J.; IUBMB Life (2019 Aug) 71:1167-1180. Abstract/Full Text
Crystal structure of an adenovirus virus-associated RNA.: Hood IV, Gordon JM, Bou-Nader C, Henderson FE, Bahmanjah S, Zhang J.; Nat Commun (2019 Jun 28) 10:2871. Abstract/Full Text
The search for a PKR code-differential regulation of protein kinase R activity by diverse RNA and protein regulators.: Bou-Nader C, Gordon JM, Henderson FE, Zhang J.; RNA (2019 May) 25:539-556. Abstract/Full Text
Direct modulation of T-box riboswitch-controlled transcription by protein synthesis inhibitors.: Stamatopoulou V, Apostolidi M, Li S, Lamprinou K, Papakyriakou A, Zhang J, Stathopoulos C.; Nucleic Acids Res (2017 Sep 29) 45:10242-10258. Abstract/Full Text
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.: Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J, Ferré-D'Amaré AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JC, Woodson SA, Wang YX.; Nature (2017 Jan 12) 541:242-246. Abstract/Full Text
A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure.: Zhang J, Landick R.; Trends Biochem Sci (2016 Apr) 41:293-310. Abstract/Full Text
Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers.: Zhang J, Ferré-DAmaré AR.; Biomolecules (2016 Apr 1) 6. Abstract/Full Text
The tRNA Elbow in Structure, Recognition and Evolution.: Zhang J, Ferré-D'Amaré AR.; Life (Basel) (2016 Jan 12) 6. Abstract/Full Text
Structure and mechanism of the T-box riboswitches.: Zhang J, Ferré-D'Amaré AR.; Wiley Interdiscip Rev RNA (2015 Jul-Aug) 6:419-33. Abstract/Full Text
Synthesis and applications of RNAs with position-selective labelling and mosaic composition.: Liu Y, Holmstrom E, Zhang J, Yu P, Wang J, Dyba MA, Chen D, Ying J, Lockett S, Nesbitt DJ, Ferré-D'Amaré AR, Sousa R, Stagno JR, Wang YX.; Nature (2015 Jun 18) 522:368-72. Abstract/Full Text
Interaction between the tRNA-binding and C-terminal domains of Yeast Gcn2 regulates kinase activity in vivo.: Lageix S, Zhang J, Rothenburg S, Hinnebusch AG.; PLoS Genet (2015 Feb) 11:e1004991. Abstract/Full Text
Post-crystallization Improvement of RNA Crystal Diffraction Quality.: Zhang J, Ferré-D'Amaré AR.; Methods Mol Biol (2015) 1316:13-24. Abstract/Full Text
Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase.: Windgassen TA, Mooney RA, Nayak D, Palangat M, Zhang J, Landick R.; Nucleic Acids Res (2014 Nov 10) 42:12707-21. Abstract/Full Text
Global analysis of riboswitches by small-angle X-ray scattering and calorimetry.: Zhang J, Jones CP, Ferré-D'Amaré AR.; Biochim Biophys Acta (2014 Oct) 1839:1020-1029. Abstract/Full Text
Dramatic improvement of crystals of large RNAs by cation replacement and dehydration.: Zhang J, Ferré-D'Amaré AR.; Structure (2014 Sep 2) 22:1363-1371. Abstract/Full Text
Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout.: Zhang J, Ferré-D'Amaré AR.; Mol Cell (2014 Jul 3) 55:148-55. Abstract/Full Text
New molecular engineering approaches for crystallographic studies of large RNAs.: Zhang J, Ferré-D'Amaré AR.; Curr Opin Struct Biol (2014 Jun) 26:9-15. Abstract/Full Text
A flexible, scalable method for preparation of homogeneous aminoacylated tRNAs.: Zhang J, Ferré-D'Amaré AR.; Methods Enzymol (2014) 549:105-13. Abstract/Full Text
Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.: Zhang J, Ferré-D'Amaré AR.; Nature (2013 Aug 15) 500:363-6. Abstract/Full Text
YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.: Baird NJ, Zhang J, Hamma T, Ferré-D'Amaré AR.; RNA (2012 Apr) 18:759-70. Abstract/Full Text
Role of the RNA polymerase trigger loop in catalysis and pausing.: Zhang J, Palangat M, Landick R.; Nat Struct Mol Biol (2010 Jan) 17:99-104. Abstract/Full Text
A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing.: Toulokhonov I, Zhang J, Palangat M, Landick R.; Mol Cell (2007 Aug 3) 27:406-19. Abstract/Full Text
Structural basis for substrate loading in bacterial RNA polymerase.: Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R.; Nature (2007 Jul 12) 448:163-8. Abstract/Full Text

Last Reviewed June 2024