2024
Structural basis for transcription activation by the nitrate-responsive regulator NarL
Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B. Structural basis for transcription activation by the nitrate-responsive regulator NarL. Nucleic Acids Research 2024, 52: 1471-1482. PMID: 38197271, PMCID: PMC10853779, DOI: 10.1093/nar/gkad1231.Peer-Reviewed Original ResearchTranscription activation complexC-terminal domainTranscription activationAlpha C-terminal domainStructural basisGlobal transcription factorCryo-EM structureDetailed mechanistic understandingPromoter DNATranscription initiationBinds DNATranscription assaysTranscription factorsActivation complexÅ resolutionNarLDimer bindsMolecular mechanismsNovel mechanismActivation mechanismMechanistic understandingDNAStress factorsPromoterActivation
2022
A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6
Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F. A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6. Nature Communications 2022, 13: 1059. PMID: 35217664, PMCID: PMC8881611, DOI: 10.1038/s41467-022-28695-w.Peer-Reviewed Original ResearchConceptsOrigin recognition complexS. cerevisiaeCyclin-dependent kinase phosphorylationMcm2-7 loadingN-terminal domainCryo-electron microscopyCDK phosphorylationRecognition complexDNA replicationReplication originsÅ resolutionKinase phosphorylationMechanism of originCdc6Coordinated actionCerevisiaePhosphorylationDNAInhibitory signalsStructural detailsSite regulationRecruitmentOrc6AssemblyCdt1Single particle cryo-EM structure of the outer hair cell motor protein prestin
Butan C, Song Q, Bai JP, Tan WJT, Navaratnam D, Santos-Sacchi J. Single particle cryo-EM structure of the outer hair cell motor protein prestin. Nature Communications 2022, 13: 290. PMID: 35022426, PMCID: PMC8755724, DOI: 10.1038/s41467-021-27915-z.Peer-Reviewed Original ResearchConceptsTransmembrane domainProtein prestinSingle-particle cryo-EM structuresAnti-sigma factor antagonist domainOuter hair cell motor protein prestinCryo-EM structureCryo-electron microscopyMotor protein prestinSLC26 family membersSulfate transportersTransmembrane segmentsPrestin functionÅ resolutionPrestinOHC electromotilityOpen stateCochlear amplificationPutative mechanismsFamily membersDomainRepeatsSLC26A9TransportersMutationsElectromotility
2020
Crystal structure of the C-terminal domain of DENR
Lomakin IB, De S, Wang J, Borkar AN, Steitz TA. Crystal structure of the C-terminal domain of DENR. Computational And Structural Biotechnology Journal 2020, 18: 696-704. PMID: 32257053, PMCID: PMC7114459, DOI: 10.1016/j.csbj.2020.03.009.Peer-Reviewed Original ResearchNon-canonical translation initiationTerminal domainTranslation initiationRibosomal recyclingSequence homology modelingSmall ribosomal subunitInitiation factor eIF1N-terminal domainInitiation codon selectionMCT-1Low-resolution crystal structureIon-binding sitesStable heterodimerRibosomal subunitCodon selectionÅ resolutionSimilar foldHomology modelingHelix h44EIF1DENRRRNAP siteCrystal structureHeterodimers
2019
Human keratin 1/10‐1B tetramer structures reveal a knob‐pocket mechanism in intermediate filament assembly
Eldirany SA, Ho M, Hinbest AJ, Lomakin IB, Bunick CG. Human keratin 1/10‐1B tetramer structures reveal a knob‐pocket mechanism in intermediate filament assembly. The EMBO Journal 2019, 38: embj2018100741. PMID: 31036554, PMCID: PMC6545558, DOI: 10.15252/embj.2018100741.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionCircular DichroismCrystallography, X-RayCytoskeletonDynamic Light ScatteringHumansHydrophobic and Hydrophilic InteractionsIntermediate Filament ProteinsKeratin-1Keratin-10Models, MolecularMutation, MissenseProtein FoldingProtein Interaction Domains and MotifsProtein MultimerizationProtein Structure, QuaternaryProtein Structure, SecondarySkin DiseasesConceptsFilament assemblyN-terminal hydrophobic pocketIntermediate filament assemblyTetramer assemblyÅ structureÅ resolutionCircular dichroism measurementsTetramer formationAssembly mechanismHydrophobic faceHydrophobic pocketSecondary structureOctamer structureEpidermolytic palmoplantar keratodermaKeratin filamentsIntermediate filamentsMutationsPathogenic mutationsTetramer structureDichroism measurementsAtomic resolutionAssemblyBiochemical determinantsKeratin 1/10Tetramer
2018
Cryo-EM structure of the insect olfactory receptor Orco
Butterwick JA, del Mármol J, Kim KH, Kahlson MA, Rogow JA, Walz T, Ruta V. Cryo-EM structure of the insect olfactory receptor Orco. Nature 2018, 560: 447-452. PMID: 30111839, PMCID: PMC6129982, DOI: 10.1038/s41586-018-0420-8.Peer-Reviewed Original ResearchConceptsAnchor domainOdorant receptorsSingle-particle cryo-electron microscopy structureCryo-electron microscopy structureMinimal sequence conservationReceptor familyRemarkable sequence diversityCryo-EM structureInter-subunit interactionsMicroscopy structureSequence conservationSequence diversityÅ resolutionCentral poreStructural insightsIon channelsOrcoSuch diversityOlfactory systemDiversityEnormous varietyOdor tuningFamilyInsectsSubunits
2017
Crystallographic Data Support the Carousel Mechanism of Water Supply to the Oxygen-Evolving Complex of Photosystem II
Wang J, Askerka M, Brudvig GW, Batista VS. Crystallographic Data Support the Carousel Mechanism of Water Supply to the Oxygen-Evolving Complex of Photosystem II. ACS Energy Letters 2017, 2: 2299-2306. PMID: 29057331, PMCID: PMC5644713, DOI: 10.1021/acsenergylett.7b00750.Peer-Reviewed Original ResearchOxygen-evolving complexWater ligandsQuantum mechanics/molecular mechanics analysisO bond formationPhotosystem IINew water moleculeMolecular mechanics analysisBiomimetic photocatalytic systemsDifference Fourier mapsWater moleculesPhotocatalytic cyclesCatalytic cycleSubstrate waterMn centersBond formationPhotocatalytic systemCrystallographic dataXFEL dataFourier mapsStructure-function relationsLigandsÅ resolutionComplexesNature of rearrangementsWater
2016
Extended‐Synaptotagmins as Lipid Transporters at ER‐PM Contact Sites
Reinisch K, Schauder C, Wu X, Saheki Y, Narayanaswamy P, Torta F, Wenk M, De Camilli P. Extended‐Synaptotagmins as Lipid Transporters at ER‐PM Contact Sites. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.115.2.Peer-Reviewed Original ResearchMembrane contact sitesSMP domainContact sitesExtended synaptotagminsEndoplasmic reticulumPlasma membraneER-PM contact sitesLipid transportLipid transferLipid-binding modulesER-PM tethersΒ-barrel structureExchange of lipidsERMES complexE-SytsProtein modulesProtein domainsVesicular transportC2 domainÅ resolutionLipid transportersHydrophobic residuesUehara Memorial FoundationSynaptotagmin 2Direct role
2015
Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled
Hu J, Yuan Q, Kang X, Qin Y, Li L, Ha Y, Wu D. Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled. Nature Communications 2015, 6: 8205. PMID: 26365782, PMCID: PMC4570271, DOI: 10.1038/ncomms9205.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAnimalsBinding SitesCalorimetryCatalytic DomainCircular DichroismCrystallizationCrystallography, X-RayDimerizationDishevelled ProteinsHEK293 CellsHumansPhosphatidylinositol 4,5-DiphosphatePhosphatidylinositol PhosphatesPhosphoproteinsPhosphorylationPhosphotransferases (Alcohol Group Acceptor)Protein Structure, TertiaryZebrafishConceptsSubstrate-binding siteLipid kinasesDIX domainCellular functionsCatalytic domainPhosphate kinaseÅ resolutionMutagenesis studiesRegulatory mechanismsMolecular mechanismsCatalytic activityPIP5K1AHead groupsCrystal structureSide dimerKinaseWntStructural informationRegulationDimerizationMoleculesResolution of structuresImportant rolePhosphatidylinositolType IStructure and function of the N‐terminal domain of the human mitochondrial calcium uniporter
Lee Y, Min CK, Kim TG, Song HK, Lim Y, Kim D, Shin K, Kang M, Kang JY, Youn HS, Lee JG, An JY, Park KR, Lim JJ, Kim JH, Kim JH, Park ZY, Kim YS, Wang J, Kim DH, Eom SH. Structure and function of the N‐terminal domain of the human mitochondrial calcium uniporter. EMBO Reports 2015, 16: 1318-1333. PMID: 26341627, PMCID: PMC4662854, DOI: 10.15252/embr.201540436.Peer-Reviewed Original ResearchConceptsN-terminal domainMitochondrial calcium uniporterCalcium uniporterHuman mitochondrial calcium uniporterMitochondrial calcium uptake 1CaMKII phosphorylation siteDominant negative effectCell linesMitochondrial calcium uptakePhosphorylation sitesNovel foldDeletion mutantsMCU functionÅ resolutionTumor suppressorHeLa cell lineUniporterMutantsUptake 1Calcium uptakeS92SuppressorOncogeneRegulatorDomainCrystal structure of the eukaryotic origin recognition complex
Bleichert F, Botchan MR, Berger JM. Crystal structure of the eukaryotic origin recognition complex. Nature 2015, 519: 321-326. PMID: 25762138, PMCID: PMC4368505, DOI: 10.1038/nature14239.Peer-Reviewed Original ResearchConceptsOrigin recognition complexDrosophila origin recognition complexRecognition complexEukaryotic origin recognition complexHeterohexameric origin recognition complexMini-chromosome maintenance 2Winged-helix domainCatalytic amino acidsCellular DNA replicationWinged-helix foldORC subunitsEncircles DNAHelicase loadingGenomic integrityORC functionDevelopmental controlDNA replicationÅ resolutionDomain interactionsDisrupts interactionsCell cycleMaintenance 2Amino acidsCentral channelUnanticipated features
2012
Bidentate and tridentate metal‐ion coordination states within ternary complexes of RB69 DNA polymerase
Xia S, Eom SH, Konigsberg WH, Wang J. Bidentate and tridentate metal‐ion coordination states within ternary complexes of RB69 DNA polymerase. Protein Science 2012, 21: 447-451. PMID: 22238207, PMCID: PMC3375444, DOI: 10.1002/pro.2026.Peer-Reviewed Original ResearchConceptsCoordination complexesMetal ionsCoordination stateSecond metal ionMetal ion coordinationDivalent metal ionsTernary complexTridentate coordinationBond formationPhosphorus atomActive siteRelevant conformationsStructural studiesSelectivity mechanismIonsTriphosphate tailComplexesRB69 DNA polymeraseÅ resolutionBase selectivityGround stateSubstrate alignmentPolymerase active siteCatalysisCoordination
2011
Structural–Functional Role of Chloride in Photosystem II
Rivalta I, Amin M, Luber S, Vassiliev S, Pokhrel R, Umena Y, Kawakami K, Shen JR, Kamiya N, Bruce D, Brudvig GW, Gunner MR, Batista VS. Structural–Functional Role of Chloride in Photosystem II. Biochemistry 2011, 50: 6312-6315. PMID: 21678923, PMCID: PMC3140697, DOI: 10.1021/bi200685w.Peer-Reviewed Original ResearchAncylostoma ceylanicum Excretory–Secretory Protein 2 Adopts a Netrin-Like Fold and Defines a Novel Family of Nematode Proteins
Kucera K, Harrison LM, Cappello M, Modis Y. Ancylostoma ceylanicum Excretory–Secretory Protein 2 Adopts a Netrin-Like Fold and Defines a Novel Family of Nematode Proteins. Journal Of Molecular Biology 2011, 408: 9-17. PMID: 21352830, PMCID: PMC3070796, DOI: 10.1016/j.jmb.2011.02.033.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAncylostomaAncylostomatoideaAncylostomiasisAnimalsComplement System ProteinsHelminth ProteinsHumansMatrix MetalloproteinasesMolecular Sequence DataNerve Growth FactorsNetrin-1Protein ConformationProtein FoldingSequence Homology, Amino AcidTissue Inhibitor of MetalloproteinasesTumor Suppressor ProteinsConceptsMatrix metalloproteasesHost immune responseComplement factor C3Nematode proteinsProtein 2Complement-mediated cell lysisHookworm anaemiaMucosal vaccinesImmune responseUseful model organismFactor C3Decoy receptorDisease pathogenesisTissue inhibitorIntestinal attachmentNovel familyAncylostoma ceylanicumImmunoreactive moleculesAdult wormsGlobal healthModel organismsHookwormSequence homologyÅ resolutionHuman parasites
2001
Maintenance of an unfolded polypeptide by a cognate chaperone in bacterial type III secretion
Stebbins C, Galán J. Maintenance of an unfolded polypeptide by a cognate chaperone in bacterial type III secretion. Nature 2001, 414: 77-81. PMID: 11689946, DOI: 10.1038/35102073.Peer-Reviewed Original ResearchConceptsEffector proteinsSecretion systemType III protein secretion systemBacterial type III secretionSpecific cytosolic chaperonesSuch effector proteinsType III secretion systemSecretion-competent stateVirulence effector proteinsProtein secretion systemChaperone-binding domainHost cell cytosolType III secretionType III apparatusCytosolic chaperonesUnfolded polypeptidesSecretion machineryCognate chaperoneÅ resolutionChaperonesCell cytosolChaperone moleculesEffective translocationBacterial pathogensHydrophobic interface
1999
Bound-solvent structures for microgravity-, ground control-, gel- and microbatch-grown hen egg-white lysozyme crystals at 1.8 Å resolution
Dong J, Boggon T, Chayen N, Raftery J, Bi R, Helliwell J. Bound-solvent structures for microgravity-, ground control-, gel- and microbatch-grown hen egg-white lysozyme crystals at 1.8 Å resolution. Acta Crystallographica Section D, Structural Biology 1999, 55: 745-52. PMID: 10089304, DOI: 10.1107/s0907444998016047.Peer-Reviewed Original ResearchConceptsHen egg white lysozymeX-ray dataAdvanced Protein Crystallization FacilityDifferent crystallization methodsLysozyme crystalsCrystal growth environmentProtein structureHen egg-white lysozyme crystalsEgg white lysozymeCrystallization methodProtein crystalsGelÅ resolutionCrystalsMicrogravity Spacelab (LMS) missionCrystallizationCrystallization FacilityAgarose gelStructureDiffusion methodPhase boundaryPhysics statesOilNumber of methodsLysozyme
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