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Jack Zhang, PhD

Assistant Professor of Molecular Biophysics and Biochemistry

Contact Information

Jack Zhang, PhD

Mailing Address

  • Molecular Biophysics and Biochemistry

    260 Whitney Avenue, Yale Science Building

    New Haven, CT 06511

    United States

The Zhang Lab

Research Summary

Our lab focuses on the structural mechanisms of motor proteins and cryo-electron microscopy (cryo-EM) methods. The long-term goal is to reveal the mechanisms of high-level cellular activities driven by motor proteins from a structure perspective at the atomic level. We are particularly interested in dyneins and many related protein complexes for their fascinating roles in intracellular/intraflagellar transport, cell division, organelle positioning, cell motility, neurodevelopment, neurodegeneration, viral infection and the mechanisms of dynein activity regulation during these processes. In addition to dynein mechanisms, we are also passionate about cryo-EM/ET methodology development and interdisciplinary researches in depth to enable the visualization of atomic details of large, dynamic protein complexes in vitro and in situ.

Coauthors

Research Interests

Biochemistry; Biophysics; Cilia; Cytoskeleton; Dyneins; Flagella; Image Processing, Computer-Assisted; Microscopy, Electron; Microscopy, Fluorescence; Microtubules; Molecular Biology; Nervous System Diseases; Protein Conformation; Signal Processing, Computer-Assisted; Tomography; Protein Structure, Tertiary; Cryoelectron Microscopy; Imaging, Three-Dimensional; Axoneme; Axonemal Dyneins; Machine Learning

Research Image

A brief view of cryo-EM flow chart

A brief view of cryo-EM flow chart

Selected Publications

  • Cryo-EM structure of an active central apparatus.Han L, Rao Q, Yang R, Wang Y, Chai P, Xiong Y, Zhang K. Cryo-EM structure of an active central apparatus. Nature Structural & Molecular Biology 2022, 29: 472-482. PMID: 35578022, PMCID: PMC9113940, DOI: 10.1038/s41594-022-00769-9.
  • Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R. Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118 PMID: 34417297, PMCID: PMC8403832, DOI: 10.1073/pnas.2106750118.
  • Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism.Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K. Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism. Nature Structural & Molecular Biology 2021, 28: 799-810. PMID: 34556869, PMCID: PMC8500839, DOI: 10.1038/s41594-021-00656-9.
  • NLRP6 self-assembles into a linear molecular platform following LPS binding and ATP stimulation.Leng F, Yin H, Qin S, Zhang K, Guan Y, Fang R, Wang H, Li G, Jiang Z, Sun F, Wang DC, Xie C. NLRP6 self-assembles into a linear molecular platform following LPS binding and ATP stimulation. Scientific Reports 2020, 10: 198. PMID: 31932628, PMCID: PMC6957519, DOI: 10.1038/s41598-019-57043-0.
  • New interfaces on MiD51 for Drp1 recruitment and regulation.Ma J, Zhai Y, Chen M, Zhang K, Chen Q, Pang X, Sun F. New interfaces on MiD51 for Drp1 recruitment and regulation. PloS One 2019, 14: e0211459. PMID: 30703167, PMCID: PMC6355003, DOI: 10.1371/journal.pone.0211459.
  • Structural basis of antagonism of human APOBEC3F by HIV-1 Vif.Hu Y, Desimmie BA, Nguyen HC, Ziegler SJ, Cheng TC, Chen J, Wang J, Wang H, Zhang K, Pathak VK, Xiong Y. Structural basis of antagonism of human APOBEC3F by HIV-1 Vif. Nature Structural & Molecular Biology 2019, 26: 1176-1183. PMID: 31792451, PMCID: PMC6899190, DOI: 10.1038/s41594-019-0343-6.
  • Towards dynamic structure of biological complexes at atomic resolution by cryo-EMZhang K. "Towards dynamic structure of biological complexes at atomic resolution by cryo-EM." Chin. Phys. B 2018. 27(6): 66801-066801.
  • A brief introduction of cryo-EM revolution-the Nobel Prize in Chemistry 2017.Zhang K, Liu Z. A brief introduction of cryo-EM revolution-the Nobel Prize in Chemistry 2017. Science China. Life Sciences 2018, 61: 368-370. PMID: 29318502, DOI: 10.1007/s11427-017-9215-3.
  • Crystal structure of E. coli apolipoprotein N-acyl transferase.Lu G, Xu Y, Zhang K, Xiong Y, Li H, Cui L, Wang X, Lou J, Zhai Y, Sun F, Zhang XC. Crystal structure of E. coli apolipoprotein N-acyl transferase. Nature Communications 2017, 8: 15948. PMID: 28885614, PMCID: PMC5500890, DOI: 10.1038/ncomms15948.
  • Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.Zhang K, Foster HE, Rondelet A, Lacey SE, Bahi-Buisson N, Bird AW, Carter AP. Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated. Cell 2017, 169: 1303-1314.e18. PMID: 28602352, PMCID: PMC5473941, DOI: 10.1016/j.cell.2017.05.025.
  • FIRT: Filtered iterative reconstruction technique with information restoration.Chen Y, Zhang Y, Zhang K, Deng Y, Wang S, Zhang F, Sun F. FIRT: Filtered iterative reconstruction technique with information restoration. Journal Of Structural Biology 2016, 195: 49-61. PMID: 27134004, DOI: 10.1016/j.jsb.2016.04.015.
  • Gctf: Real-time CTF determination and correction.Zhang K. Gctf: Real-time CTF determination and correction. Journal Of Structural Biology 2016, 193: 1-12. PMID: 26592709, PMCID: PMC4711343, DOI: 10.1016/j.jsb.2015.11.003.
  • The structure of the dynactin complex and its interaction with dynein.Urnavicius L, Zhang K, Diamant AG, Motz C, Schlager MA, Yu M, Patel NA, Robinson CV, Carter AP. The structure of the dynactin complex and its interaction with dynein. Science (New York, N.Y.) 2015, 347: 1441-1446. PMID: 25814576, PMCID: PMC4413427, DOI: 10.1126/science.aaa4080.
  • Cryo-EM structures of two bovine adenovirus type 3 intermediates.Cheng L, Huang X, Li X, Xiong W, Sun W, Yang C, Zhang K, Wang Y, Liu H, Huang X, Ji G, Sun F, Zheng C, Zhu P. Cryo-EM structures of two bovine adenovirus type 3 intermediates. Virology 2014, 450-451: 174-81. PMID: 24503080, DOI: 10.1016/j.virol.2013.12.012.
  • C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation.Qiu B, Zhang K, Wang S, Sun F. C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation. Biochemical And Biophysical Research Communications 2014, 446: 380-6. PMID: 24613384, DOI: 10.1016/j.bbrc.2014.02.125.
  • A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature.Pang X, Fan J, Zhang Y, Zhang K, Gao B, Ma J, Li J, Deng Y, Zhou Q, Egelman EH, Hsu VW, Sun F. A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature. Developmental Cell 2014, 31: 73-86. PMID: 25284369, PMCID: PMC4198613, DOI: 10.1016/j.devcel.2014.08.020.
  • Identification of SERPINB1 as a physiological inhibitor of human granzyme H.Wang L, Li Q, Wu L, Liu S, Zhang Y, Yang X, Zhu P, Zhang H, Zhang K, Lou J, Liu P, Tong L, Sun F, Fan Z. Identification of SERPINB1 as a physiological inhibitor of human granzyme H. Journal Of Immunology (Baltimore, Md. : 1950) 2013, 190: 1319-30. PMID: 23269243, DOI: 10.4049/jimmunol.1202542.
  • Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.Wang X, Xu F, Liu J, Gao B, Liu Y, Zhai Y, Ma J, Zhang K, Baker TS, Schulten K, Zheng D, Pang H, Sun F. Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography. PLoS Pathogens 2013, 9: e1003132. PMID: 23341770, PMCID: PMC3547835, DOI: 10.1371/journal.ppat.1003132.
  • Structural insights into the intrinsic self-assembly of Par-3 N-terminal domain.Zhang Y, Wang W, Chen J, Zhang K, Gao F, Gao B, Zhang S, Dong M, Besenbacher F, Gong W, Zhang M, Sun F, Feng W. Structural insights into the intrinsic self-assembly of Par-3 N-terminal domain. Structure (London, England : 1993) 2013, 21: 997-1006. PMID: 23643951, DOI: 10.1016/j.str.2013.04.004.
  • Flexible interwoven termini determine the thermal stability of thermosomes.Zhang K, Wang L, Liu Y, Chan KY, Pang X, Schulten K, Dong Z, Sun F. Flexible interwoven termini determine the thermal stability of thermosomes. Protein & Cell 2013, 4: 432-44. PMID: 23709365, PMCID: PMC3740188, DOI: 10.1007/s13238-013-3026-9.
  • Structure reveals regulatory mechanisms of a MaoC-like hydratase from Phytophthora capsici involved in biosynthesis of polyhydroxyalkanoates (PHAs).Wang H, Zhang K, Zhu J, Song W, Zhao L, Zhang X. Structure reveals regulatory mechanisms of a MaoC-like hydratase from Phytophthora capsici involved in biosynthesis of polyhydroxyalkanoates (PHAs). PloS One 2013, 8: e80024. PMID: 24244597, PMCID: PMC3823801, DOI: 10.1371/journal.pone.0080024.
  • Mechanistic insights into regulated cargo binding by ACAP1 protein.Bai M, Pang X, Lou J, Zhou Q, Zhang K, Ma J, Li J, Sun F, Hsu VW. Mechanistic insights into regulated cargo binding by ACAP1 protein. The Journal Of Biological Chemistry 2012, 287: 28675-85. PMID: 22645133, PMCID: PMC3436524, DOI: 10.1074/jbc.M112.378810.
  • Structural insights into the substrate specificity of human granzyme H: the functional roles of a novel RKR motif.Wang L, Zhang K, Wu L, Liu S, Zhang H, Zhou Q, Tong L, Sun F, Fan Z. Structural insights into the substrate specificity of human granzyme H: the functional roles of a novel RKR motif. Journal Of Immunology (Baltimore, Md. : 1950) 2012, 188: 765-73. PMID: 22156497, DOI: 10.4049/jimmunol.1101381.
  • Cryo-EM structure of a transcribing cypovirus.Yang C, Ji G, Liu H, Zhang K, Liu G, Sun F, Zhu P, Cheng L. Cryo-EM structure of a transcribing cypovirus. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 6118-23. PMID: 22492979, PMCID: PMC3341035, DOI: 10.1073/pnas.1200206109.
  • Substrate Binding Properties of Thermosome ATcpn-β from Acidianus TengchongensisWang L, Zhang K, Fan Z, Dong Z, and Sun F. Substrate Binding Properties of Thermosome ATcpnβ from Acidianus Tengchongensis. Progress in Biochemistry and Biophysics 2011, 38:151-158.
  • ATOM 1.0: A GPU Powered Package for Electron Tomography Reconstruction.Chu Q, Zhang K, Wan X, Zhang C, Zhang G, Shen B, Liu X, Zhao K, Chu X, Zhang F, Sun F. ATOM 1.0: A GPU Powered Package for Electron Tomography Reconstruction. Acta Biophys Sin 2011, 27:231-241.
  • Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping.Cheng L, Sun J, Zhang K, Mou Z, Huang X, Ji G, Sun F, Zhang J, Zhu P. Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 1373-8. PMID: 21220303, PMCID: PMC3029759, DOI: 10.1073/pnas.1014995108.
  • Autotransporter passenger domain secretion requires a hydrophobic cavity at the extracellular entrance of the β-domain pore.Zhai Y, Zhang K, Huo Y, Zhu Y, Zhou Q, Lu J, Black I, Pang X, Roszak AW, Zhang X, Isaacs NW, Sun F. Autotransporter passenger domain secretion requires a hydrophobic cavity at the extracellular entrance of the β-domain pore. The Biochemical Journal 2011, 435: 577-87. PMID: 21306302, DOI: 10.1042/BJ20101548.
  • Crystal structure of a novel esterase Rv0045c from Mycobacterium tuberculosis.Zheng X, Guo J, Xu L, Li H, Zhang D, Zhang K, Sun F, Wen T, Liu S, Pang H. Crystal structure of a novel esterase Rv0045c from Mycobacterium tuberculosis. PloS One 2011, 6: e20506. PMID: 21637775, PMCID: PMC3102732, DOI: 10.1371/journal.pone.0020506.
  • Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography.Wan X, Zhang F, Chu Q, Zhang K, Sun F, Yuan B, Liu Z. Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography. Journal Of Structural Biology 2011, 175: 277-87. PMID: 21699984, DOI: 10.1016/j.jsb.2011.06.002.
  • Development and Frontier of Electron Microscopy 3D Reconstruction.Zhang K, Zhang Y, Hu Z, Ji G, and Sun F. Development and Frontier of Electron Microscopy 3D Reconstruction. Acta Biophys Sin 2010, 26:533-559.
  • Cloning, Expression, Purification and Preliminary Crystallographic Analysis of Caenorhabditis elegans Enoyl-CoA Hydratase.Li Z, Zhang K, Zhai Y, Zhou Q, Geng Y, and Sun F. Cloning, Expression, Purification and Preliminary Crystallographic Analysis of Caenorhabditis elegans Enoyl-CoA Hydratase. Acta Biophys Sin 2010, 26:37-48.
  • Five mutations in N-terminus confer thermostability on mesophilic xylanase.Zhang S, Zhang K, Chen X, Chu X, Sun F, Dong Z. Five mutations in N-terminus confer thermostability on mesophilic xylanase. Biochemical And Biophysical Research Communications 2010, 395: 200-6. PMID: 20361933, DOI: 10.1016/j.bbrc.2010.03.159.
  • Crystal structure of group II chaperonin in the open state.Huo Y, Hu Z, Zhang K, Wang L, Zhai Y, Zhou Q, Lander G, Zhu J, He Y, Pang X, Xu W, Bartlam M, Dong Z, Sun F. Crystal structure of group II chaperonin in the open state. Structure (London, England : 1993) 2010, 18: 1270-9. PMID: 20947016, PMCID: PMC3048791, DOI: 10.1016/j.str.2010.07.009.
  • Disclosing the Structure and Function of Translation MachineZhang K, Zhang C, and Sun F. Disclosing the Structure and Function of Translation Machine—Introduction of the Nobel Prize in Chemistry 2009. Acta Biophys Sin 2009, 25:325-334.
  • 3D Structural Investigation of Caveolae From Porcine Aorta Endothelial Cell by Electron Tomography.Sun S, Zhang K, Xu W, Wang G, Chen J, and Sun F. 3D Structural Investigation of Caveolae From Porcine Aorta Endothelial Cell by Electron Tomography. Progress in Biochemistry and Biophysics 2009, 36:729-735.
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