2024
High-resolution in situ structures of mammalian respiratory supercomplexes
Zheng W, Chai P, Zhu J, Zhang K. High-resolution in situ structures of mammalian respiratory supercomplexes. Nature 2024, 631: 232-239. PMID: 38811722, PMCID: PMC11222160, DOI: 10.1038/s41586-024-07488-9.Peer-Reviewed Original ResearchRespiratory supercomplexesInner membraneAssembly of respiratory supercomplexesComplex IResponse to environmental changesMitochondrial respiratory supercomplexesStructural studiesATP energy productionSupercomplex organizationAtomic-level detailsHigher-order arraysSubcellular contextNative membrane environmentReactive intermediatesOxidative phosphorylationSupercomplexStructural comparisonMolecular mechanismsAtomic detailIn situ structureMembrane environmentConformational statesNative stateSurrounding membraneEnvironmental changes
2023
LRRC23 truncation impairs radial spoke 3 head assembly and sperm motility underlying male infertility
Hwang J, Chai P, Nawaz S, Choi J, Lopez-Giraldez F, Hussain S, Bilguvar K, Mane S, Lifton R, Ahmad W, Zhang K, Chung J. LRRC23 truncation impairs radial spoke 3 head assembly and sperm motility underlying male infertility. ELife 2023, 12: rp90095. PMID: 38091523, PMCID: PMC10721216, DOI: 10.7554/elife.90095.Peer-Reviewed Original ResearchCryo-EM reveals how the mastigoneme assembles and responds to environmental signal changes
Wang Y, Yang J, Hu F, Yang Y, Huang K, Zhang K. Cryo-EM reveals how the mastigoneme assembles and responds to environmental signal changes. Journal Of Cell Biology 2023, 222: e202301066. PMID: 37882754, PMCID: PMC10602792, DOI: 10.1083/jcb.202301066.Peer-Reviewed Original ResearchConceptsSingle-particle cryo-electron microscopy structureCryo-electron microscopy structureNon-polar filamentsImmunoglobulin-like domainsDistal regionPolyproline II helixMicroscopy structureChlamydomonas reinhardtiiFlagellar motilityVaried environmental conditionsCryo-EMCell swimmingMotility controlEnvironmental responsesDisulfide bondsEnvironmental conditionsSushi domainMastigonemesThread-like structuresRedox shiftSignal sensingPotential roleProtistsReinhardtiiMST1Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation
Duan D, Lyu W, Chai P, Ma S, Wu K, Wu C, Xiong Y, Sestan N, Zhang K, Koleske A. Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation. Current Biology 2023, 33: 4582-4598.e10. PMID: 37858340, PMCID: PMC10877310, DOI: 10.1016/j.cub.2023.09.018.Peer-Reviewed Original ResearchConceptsCOS-7 cellsMT nucleationMT latticeFamily kinasesTubulin recruitmentLiquid-liquid phase separationTubulin C-terminal tailsCryo-EM analysisC-terminal tailAbl family kinasesWild-type cellsC-terminal halfRescue frequencyGenetic experimentsNeuronal morphogenesisMicrotubule nucleationSplice isoformsMicrotubule dynamicsNocodazole treatmentMolecular mechanismsAxon guidanceCell migrationDamage sitesABL2MT assemblyMicrotubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport
Ton W, Wang Y, Chai P, Beauchamp-Perez C, Flint N, Lammers L, Xiong H, Zhang K, Markus S. Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. Nature Structural & Molecular Biology 2023, 30: 1365-1379. PMID: 37322240, PMCID: PMC10590275, DOI: 10.1038/s41594-023-01010-x.Peer-Reviewed Original ResearchConceptsCryo-EM structureCargo transportProtein Lis1Human dyneinDynein mutantsCytoplasmic dyneinStructural insightsDynein activityIntracellular localizationCritical regulatorDynein activationLIS1Conformational changesDyneinMotor domainMutantsBindingHigh affinityAffinityYeastMicrotubulesRegulatorRegulationTransportActivationNew frontier of cryo-electron microscopy technology
Sun F, Zhang X, Zhang K. New frontier of cryo-electron microscopy technology. Journal Of Molecular Biology 2023, 435: 168098. PMID: 37061087, DOI: 10.1016/j.jmb.2023.168098.Peer-Reviewed Original ResearchAuthor Correction: Cryo-EM structure of an active central apparatus
Han L, Rao Q, Yang R, Wang Y, Chai P, Xiong Y, Zhang K. Author Correction: Cryo-EM structure of an active central apparatus. Nature Structural & Molecular Biology 2023, 30: 564-564. PMID: 36899097, PMCID: PMC10113143, DOI: 10.1038/s41594-023-00961-5.Peer-Reviewed Original ResearchHigh-Resolution Structural Analysis of Dyneins by Cryo-electron Microscopy
Chai P, Rao Q, Wang Y, Zhang K. High-Resolution Structural Analysis of Dyneins by Cryo-electron Microscopy. Methods In Molecular Biology 2023, 2623: 257-279. PMID: 36602691, PMCID: PMC10371436, DOI: 10.1007/978-1-0716-2958-1_16.ChaptersConceptsCryo-electron microscopyHigh-resolution structural informationLarge molecular machineHigh-resolution structuresCryo-EM approachResolution structural analysisProtein complexesStructural biologistsCellular cargoMolecular machinesDyneinDepth mechanistic understandingMolecular motorsMechanistic understandingCiliary motilityFlexible conformationIntricate architectureStructural informationMacromolecular structureForce generatorStructural analysisBiologistsSimilar structureCargoMicroscopy
2022
Structures of the CcmABCD heme release complex at multiple states
Li J, Zheng W, Gu M, Han L, Luo Y, Yu K, Sun M, Zong Y, Ma X, Liu B, Lowder EP, Mendez DL, Kranz RG, Zhang K, Zhu J. Structures of the CcmABCD heme release complex at multiple states. Nature Communications 2022, 13: 6422. PMID: 36307425, PMCID: PMC9616876, DOI: 10.1038/s41467-022-34136-5.Peer-Reviewed Original ResearchConceptsHigh-resolution cryo-EM structuresResolution cryo-EM structureABC transporter complexAttachment of hemeCryo-EM structureLarge membrane complexesHeme-binding siteATP-binding siteATP-dependent releaseTransfer of hemeC-type cytochromesHeme chaperoneHeme traffickingCytochrome c proteinMembrane proteinsHeme transferTransporter complexMembrane complexATP hydrolysisStructural basisC proteinAMP-PNPFunctional studiesHeme releaseUnbound formMulti-curve fitting and tubulin-lattice signal removal for structure determination of large microtubule-based motors
Chai P, Rao Q, Zhang K. Multi-curve fitting and tubulin-lattice signal removal for structure determination of large microtubule-based motors. Journal Of Structural Biology 2022, 214: 107897. PMID: 36089228, PMCID: PMC10321216, DOI: 10.1016/j.jsb.2022.107897.Peer-Reviewed Original ResearchIdentification of lipid droplets in gut bacteria
Zhang K, Zhou C, Li Z, Li X, Zhou Z, Cheng L, Mirza A, Shi Y, Chen B, Zhang M, Cui L, Zhang C, Wei T, Zhang X, Zhang S, Liu P. Identification of lipid droplets in gut bacteria. Protein & Cell 2022, 14: 143-148. PMID: 36929002, PMCID: PMC10019568, DOI: 10.1093/procel/pwac015.Peer-Reviewed Original ResearchCryo-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.Peer-Reviewed Original ResearchConceptsCentral apparatusDiverse cellular activitiesKinesin-like proteinCryo-EM structureArmadillo repeat proteinsCryo-electron microscopyHigh-resolution structuresEukaryotic speciesProtein subunitsMotile ciliaBridge proteinsPair of microtubulesRegulatory roleCellular activitiesProteinDynamic conformational behaviorCiliary motilityCiliaCiliary beatingStructural frameworkConformational behaviorSubunitsMicrotubulesRegulatorSpeciesStructures of the CcmABCD heme release complex at multiple statesStructures of the CcmABCD heme release complex at multiple states
Li L, Zheng W, Gu M, Han L, Luo Y, Yu K, Sun M, Zong Y, Ma X, Liu B, Lowder EP, Mendez DL, Kranz RG, Zhang K, Zhu J. Nature Communications, 2022, 13: 6422Peer-Reviewed Original Research
2021
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.Peer-Reviewed Original ResearchConceptsOuter arm dyneinMicrotubule doubletsDistinct microtubule-binding domainsHigh-resolution structuresAction of dyneinsMicrotubule-binding domainNative tracksATP hydrolysisDynein motorsHydrolyze ATPConformational changesNucleotide cycleMotor coordination mechanismATP turnoverDyneinHead interactionsMechanical forcesCryo-EM structures of Escherichia coli cytochrome bo3 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 bo3 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: e2106750118. PMID: 34417297, PMCID: PMC8403832, DOI: 10.1073/pnas.2106750118.Peer-Reviewed Original ResearchConceptsHydrogen bondsMembrane scaffold protein (MSP) nanodiscsSide chainsMetal redox centerCryo-EM structureInternal water moleculesEscherichia coli cytochrome bo3Facilitate proton transferImidazole side chainIsoprene side chainAccess of waterCryogenic electron microscopyRedox centersWater moleculesProton transferSubunit IAqueous phaseConformation 1Respiratory cytochromesRelated cytochromesHydrophobic grooveUbiquinol oxidaseQuinol oxidaseCytochrome bo3Computational studyCryo‐EM Structures of Outer‐arm Dynein Array Bound to Microtubule Doublet Reveal a Mechanism for Motor Coordination
Rao Q, Wang Y, Chai P, Kuo Y, Han L, Yang R, Yang Y, Howard J, Zhang K. Cryo‐EM Structures of Outer‐arm Dynein Array Bound to Microtubule Doublet Reveal a Mechanism for Motor Coordination. The FASEB Journal 2021, 35 DOI: 10.1096/fasebj.2021.35.s1.03099.Peer-Reviewed Original ResearchOuter arm dyneinMicrotubule-bound stateInner arm dyneinsCentral pair complexMicrotubule-binding domainMicrotubule doubletsIntermediate chainATP hydrolysisFundamental cellular processesHeavy chainCryo-EM structureCryo-EM analysisCryo-electron tomographyKey motor proteinCryo-electron microscopyLight chainCellular processesEukaryotic ciliaT. thermophilaEmbryonic developmentAdjacent microtubule doubletsCellular motilityMotor proteinsAxonemal dyneinsMotile cilia
2020
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.Peer-Reviewed Original ResearchConceptsNOD-like receptorsGlobal conformational changesStep-activation mechanismOuter membraneMolecular platformStructural basisAssembly patternsLigand specificityConformational changesInnate immune responseImmune receptorsActivation mechanismIntestinal homeostasisNegative bacteriaATP stimulationPathogen productsIntestinal tumorigenesisHigher molecular structuresMajor componentNLRP6Important roleHomodimerReceptorsCytosolImmune response
2019
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.Peer-Reviewed Original ResearchConceptsHIV-1 VifProtein degradation machineryCryo-EM structureHuman immunodeficiency virus type 1 (HIV-1) replicationCore-binding factor betaUbiquitin-proteasome pathwayRole of CbfβHIV-1 virion infectivity factorType 1 replicationVif-A3 interactionsViral immune evasionDegradation machineryAntiviral APOBEC3Terminal domainVirion infectivity factorStructural basisMolecular mechanismsViral restrictionA3 proteinsMolecular determinantsImmune evasionInfectivity factorFactor betaCellular studiesAntiviral therapeuticsNew 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.Peer-Reviewed Original Research
2018
Towards dynamic structure of biological complexes at atomic resolution by cryo-EM
Zhang K. Towards dynamic structure of biological complexes at atomic resolution by cryo-EM. Chinese Physics B 2018, 27: 066801. DOI: 10.1088/1674-1056/27/6/066801.Peer-Reviewed Original Research