2023
Cryo-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 roleProtistsReinhardtiiMST1New 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 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
Multi-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 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 behaviorSubunitsMicrotubulesRegulatorSpecies
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 ResearchMeSH KeywordsAdenosine TriphosphateCryoelectron MicroscopyDyneinsMicrotubulesModels, MolecularTetrahymena thermophilaConceptsOuter 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 study
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 therapeutics
2018
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.Peer-Reviewed Original Research
2017
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.Peer-Reviewed Original ResearchConceptsStructure-based mutagenesisCryoelectron microscopy structureCargo adaptor proteinsMicroscopy structureAdaptor proteinCytoplasmic dyneinMicrotubule affinityCryo-EMDynein 1DynactinOpen formDynein tailInhibited stateProcessive movementMotor domainMicrotubulesMotor dimerizationTransport machinesHigh affinityMutagenesisDyneinTailAffinityProteinDimerization
2015
Gctf: Real-time CTF determination and correction
Zhang K. Gctf: Real-time CTF determination and correction. Journal Of Structural Biology 2015, 193: 1-12. PMID: 26592709, PMCID: PMC4711343, DOI: 10.1016/j.jsb.2015.11.003.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsCryoelectron MicroscopyImage Processing, Computer-AssistedImaging, Three-DimensionalSoftwareConceptsCTF determinationSubsequent image processingGPU accelerationImage processingCTF parametersBackground subtractionLocal defocusSingle frameNovel diagnosis methodDiagnosis methodVerification procedureIndependent programsNovel approachRepresentative datasetLogarithmic amplitude spectrumObserved micrographsComputer programContrast transfer functionGPUPractical useAccurate estimationDatasetSoftwareRELIONFREALIGNThe 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 2015, 347: 1441-1446. PMID: 25814576, PMCID: PMC4413427, DOI: 10.1126/science.aaa4080.Peer-Reviewed Original ResearchConceptsDynactin complexBicaudal D2Microtubule motors cytoplasmic dynein-1Distinct protein complexesCytoplasmic dynein-1Cryo-electron microscopyProtein Arp1Protein complexesAngstrom structureDynein 1DynactinEssential cofactorΒ-actinDyneinShoulder domainDependent interactionFilamentsComplexesArp1CofactorActinCopiesInteractionPeptidesDomain
2014
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: 174-181. PMID: 24503080, DOI: 10.1016/j.virol.2013.12.012.Peer-Reviewed Original ResearchMeSH KeywordsAdenoviridae InfectionsAdenoviruses, HumanAnimalsCapsidCattleCattle DiseasesCell LineCryoelectron MicroscopyHumansMastadenovirusVirus AssemblyConceptsCryo-electron tomography analysisDNA encapsidation processCryo-EM structureCryo-electron microscopyVertebrate speciesFirst structural comparisonProtein VIDNA encapsidationEncapsidation processStructural comparisonProtein IXUnique conformationBackbone levelIntermediate structuresHuman ADMass spectrometryLater stagesEncapsidationSpeciesSimilar structureBAd3HostIntermediatesAssemblyCleavage
2013
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: 432-444. PMID: 23709365, PMCID: PMC3740188, DOI: 10.1007/s13238-013-3026-9.Peer-Reviewed Original ResearchStructural 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 2013, 21: 997-1006. PMID: 23643951, DOI: 10.1016/j.str.2013.04.004.Peer-Reviewed Original ResearchConceptsN-terminal domainPAR-3PAR-3/PARCell polarity establishmentPolarity establishmentEpithelial polarizationScaffold proteinProtein domainsLongitudinal packingStructural basisStructural insightsCryoelectron microscopyCentral organizerFilament-like structuresC complexFilament structureSelf-association capacitySelf-associationUnderlying mechanismDomainElectrostatic interactionsInteraction modesProteinCrystal structureAtomic 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.Peer-Reviewed Original Research
2012
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: 6118-6123. PMID: 22492979, PMCID: PMC3341035, DOI: 10.1073/pnas.1200206109.Peer-Reviewed Original ResearchMeSH KeywordsCapsidCapsid ProteinsCryoelectron MicroscopyModels, MolecularProtein ConformationProtein Structure, TertiaryReoviridaeRNA, MessengerRNA, ViralTranscription, GeneticConceptsNascent mRNATurret proteinFamily ReoviridaeCapsid shellConformational changesCapsid proteinMRNA transcriptionCryo-EM structureMajor capsid proteinGood model systemGuanylyltransferase domainTranscription cycleViral capsid proteinsIcosahedral viral capsidsCypovirusGenomic RNACryoelectron microscopyGMP moietyRNA virusesProteinViral capsidTranscriptionMRNAReoviridaeModel system
2011
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: 1373-1378. PMID: 21220303, PMCID: PMC3029759, DOI: 10.1073/pnas.1014995108.Peer-Reviewed Original ResearchConceptsCytoplasmic polyhedrosis virusDeduced amino acid sequenceCryo-EM structureRNA segment 7Amino acid sequenceMechanisms of mRNANascent mRNAEnzymatic domainsAcid sequenceCryoelectron microscopyFamily ReoviridaeProtein VP5Capsid shellPolyhedrosis virusFull atomic modelsAtomic modelStructural organizationGuanylyltransferaseMRNASegment 7ProteinCypovirus
2010
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 2010, 18: 1270-1279. PMID: 20947016, PMCID: PMC3048791, DOI: 10.1016/j.str.2010.07.009.Peer-Reviewed Original ResearchConceptsGroup II chaperoninLid domainConformational changesOpen stateATP-dependent mannerHigh-resolution structuresDetailed conformational changesFunctional cycleThermosomeHydrophobic patchStructural comparisonProtease K digestionChaperoninClosed stateK digestionCrystal structureStructural fittingOpen formComplete crystal structureClosed structureSpeciesDomainProteinATPElectron microscopy