2022
How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM
Wang J, Liu J, Gisriel CJ, Wu S, Maschietto F, Flesher DA, Lolis E, Lisi GP, Brudvig GW, Xiong Y, Batista VS. How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM. Journal Of Structural Biology 2022, 214: 107902. PMID: 36202310, PMCID: PMC10226527, DOI: 10.1016/j.jsb.2022.107902.Peer-Reviewed Original ResearchConceptsCryo-EM mapsAmino acid residuesAcid residuesCryo-electron microscopy mapIndividual amino acid residuesCyanobacteria Synechocystis spPCC 6803Synechocystis spMicroscopy mapsThermosynechococcus elongatusSARS-CoV-2 spike proteinLocal structural changesResiduesSpike proteinAtomic coordinatesElongatusSubunitsSpeciesProteinSpSimilar structureStructural changesInsight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript‑1
Wang J, Sachpatzidis A, Christian TD, Lomakin IB, Garen A, Konigsberg WH. Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript‑1. Biochemistry 2022, 61: 1723-1734. PMID: 35998361, DOI: 10.1021/acs.biochem.2c00192.Peer-Reviewed Original ResearchConceptsRNA recognition motifSplicing factorsRNA bindingÅ resolution crystal structureTranscript 1DNA-binding domainRNA-binding pocketTumor suppression mechanismNew regulatory mechanismTumor suppressor proteinResolution crystal structureMurine virusesAcid proteinSuppressor proteinRecognition motifLung adenocarcinoma transcript 1Gene expressionRegulatory mechanismsApo structureRNA virusesHuman diseasesRNABinding pocketsHuman metastasesPositive cooperativityInsights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV‑2 for the Priming Reaction from Molecular Dynamics Simulations
Wang J, Shi Y, Reiss K, Allen B, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Insights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV‑2 for the Priming Reaction from Molecular Dynamics Simulations. Biochemistry 2022, 61: 424-432. PMID: 35199520, PMCID: PMC8887646, DOI: 10.1021/acs.biochem.1c00755.Peer-Reviewed Original ResearchConceptsReplication-transcription complexPriming reactionRNA duplexesTemplate strandRNA templateHigher-order oligomerizationRNA-dependent RNA polymeraseCryo-EM structureRNA primaseViral RNA templateRNA polymerasePrimer synthesisViral transcriptionSecondary structureViral genomeSubunitsMolecular dynamics simulations
2021
Identification of Mg2+ ions next to nucleotides in cryo‐EM maps using electrostatic potential maps
Wang J, Natchiar SK, Moore PB, Klaholz BP. Identification of Mg2+ ions next to nucleotides in cryo‐EM maps using electrostatic potential maps. Acta Crystallographica Section D, Structural Biology 2021, 77: 534-539. PMID: 33825713, PMCID: PMC8025889, DOI: 10.1107/s2059798321001893.Peer-Reviewed Original ResearchStructural analyses of an RNA stability element interacting with poly(A)
Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Structural analyses of an RNA stability element interacting with poly(A). Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2026656118. PMID: 33785601, PMCID: PMC8040590, DOI: 10.1073/pnas.2026656118.Peer-Reviewed Original ResearchConceptsRNA stability elementCis-acting RNA elementsGlobal conformational changesRich internal loopCryo-electron microscopyRice transposable elementsDiverse genomesDouble-helical regionsSmall-angle X-ray scatteringEne motifTransposable elementsGlobal structural changesRNA interactionsRNA stabilityBioinformatics studiesRNA elementsStability elementShort helixConformational changesDecay pathwaysInternal loopBiochemical structureTriplex structureBindingMotif
2018
Crystallographic evidence for two‐metal‐ion catalysis in human pol η
Wang J, Smithline ZB. Crystallographic evidence for two‐metal‐ion catalysis in human pol η. Protein Science 2018, 28: 439-447. PMID: 30368948, PMCID: PMC6319759, DOI: 10.1002/pro.3541.Peer-Reviewed Original ResearchConceptsMetal ionsProduct pyrophosphateChemical reactionsTwo-metal-ion catalysisTwo-metal-ion catalytic mechanismThird metal ionPhosphoryl transfer reactionsTransfer reactionsCrystallographic dataCatalytic mechanismCrystal structureCrystallographic evidenceHuman Pol ηMeal ionsIonsHuman polymerase ηCatalysisReactionComplexesSubPyrophosphateBindingProductsDNA polymeraseCrystalsStructural and biochemical insights into inhibition of human primase by citrate
Lee JG, Park KR, An JY, Kang JY, Shen H, Wang J, Eom SH. Structural and biochemical insights into inhibition of human primase by citrate. Biochemical And Biophysical Research Communications 2018, 507: 383-388. PMID: 30446220, DOI: 10.1016/j.bbrc.2018.11.047.Peer-Reviewed Original ResearchConceptsDNA replicationSmall catalytic subunitShort RNA segmentReplicative DNA polymerasesPhosphate binding siteMammalian chromosomesReplication forksCatalytic subunitAccessory subunitsBiochemical insightsOkazaki fragmentsRNA primersKey regulatorRNA segmentsBacterial enzymesHuman primasePrimaseDNA templateBase pairsDNA polymeraseInactive formDNA strandsBinding sitesPolymeraseSubunits
2017
Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1
Chase AR, Laudermilch E, Wang J, Shigematsu H, Yokoyama T, Schlieker C. Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1. Molecular Biology Of The Cell 2017, 28: 2765-2772. PMID: 28814508, PMCID: PMC5638581, DOI: 10.1091/mbc.e17-05-0281.Peer-Reviewed Original Research
2015
Comment on “Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism”
Wang J. Comment on “Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism”. Science 2015, 350: 519-519. PMID: 26516276, DOI: 10.1126/science.aab1432.Peer-Reviewed Original ResearchStructure 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 uptakeS92SuppressorOncogeneRegulatorDomain
2014
The mechanism of Torsin ATPase activation
Brown RS, Zhao C, Chase AR, Wang J, Schlieker C. The mechanism of Torsin ATPase activation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: e4822-e4831. PMID: 25352667, PMCID: PMC4234599, DOI: 10.1073/pnas.1415271111.Peer-Reviewed Original ResearchStructural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix
Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nature Structural & Molecular Biology 2014, 21: 633-640. PMID: 24952594, PMCID: PMC4096706, DOI: 10.1038/nsmb.2844.Peer-Reviewed Original Research
2010
Structural insight into the mechanisms of enveloped virus tethering by tetherin
Yang H, Wang J, Jia X, McNatt MW, Zang T, Pan B, Meng W, Wang HW, Bieniasz PD, Xiong Y. Structural insight into the mechanisms of enveloped virus tethering by tetherin. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 18428-18432. PMID: 20940320, PMCID: PMC2972963, DOI: 10.1073/pnas.1011485107.Peer-Reviewed Original ResearchAntigens, CDBase SequenceCell LineCrystallography, X-RayDimerizationDNA PrimersGPI-Linked ProteinsHIV-1HumansImmunity, InnateIn Vitro TechniquesModels, MolecularMolecular Dynamics SimulationMutagenesis, Site-DirectedMutant ProteinsProtein StabilityProtein Structure, QuaternaryProtein Structure, TertiaryRecombinant ProteinsStatic ElectricityVirus Release
2009
Impact of Novel Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutations P119S and T165A on 4′-Ethynylthymidine Analog Resistance Profile
Yang G, Paintsil E, Dutschman GE, Grill SP, Wang CJ, Wang J, Tanaka H, Hamasaki T, Baba M, Cheng YC. Impact of Novel Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutations P119S and T165A on 4′-Ethynylthymidine Analog Resistance Profile. Antimicrobial Agents And Chemotherapy 2009, 53: 4640-4646. PMID: 19704131, PMCID: PMC2772322, DOI: 10.1128/aac.00686-09.Peer-Reviewed Original ResearchApplication of general formulas for the correction of a lattice‐translocation defect in crystals of a lentiviral integrase in complex with LEDGF
Hare S, Cherepanov P, Wang J. Application of general formulas for the correction of a lattice‐translocation defect in crystals of a lentiviral integrase in complex with LEDGF. Acta Crystallographica Section D, Structural Biology 2009, 65: 966-973. PMID: 19690374, DOI: 10.1107/s0907444909023695.Peer-Reviewed Original Research
2008
A regulatable switch mediates self-association in an immunoglobulin fold
Calabrese MF, Eakin CM, Wang JM, Miranker AD. A regulatable switch mediates self-association in an immunoglobulin fold. Nature Structural & Molecular Biology 2008, 15: 965-971. PMID: 19172750, PMCID: PMC2680708, DOI: 10.1038/nsmb.1483.Peer-Reviewed Original ResearchMeSH KeywordsAmyloidAmyloidosisBeta 2-MicroglobulinCopperCrystallography, X-RayElectron Spin Resonance SpectroscopyHumansHydrophobic and Hydrophilic InteractionsImmunoglobulinsIn Vitro TechniquesModels, BiologicalModels, MolecularMultiprotein ComplexesProtein FoldingProtein Interaction Domains and MotifsProtein Structure, QuaternaryRenal DialysisMechanism of Inhibition of Human Immunodeficiency Virus Type 1 Reverse Transcriptase by a Stavudine Analogue, 4′-Ethynyl Stavudine Triphosphate
Yang G, Wang J, Cheng Y, Dutschman GE, Tanaka H, Baba M, Cheng YC. Mechanism of Inhibition of Human Immunodeficiency Virus Type 1 Reverse Transcriptase by a Stavudine Analogue, 4′-Ethynyl Stavudine Triphosphate. Antimicrobial Agents And Chemotherapy 2008, 52: 2035-2042. PMID: 18391035, PMCID: PMC2415781, DOI: 10.1128/aac.00083-08.Peer-Reviewed Original ResearchConceptsM184V mutantNucleoside reverse transcriptase inhibitorHuman immunodeficiency virus type 1Immunodeficiency virus type 1Human immunodeficiency virus type 1 reverse transcriptaseReverse transcriptase inhibitorType 1 reverse transcriptaseVirus type 1Mechanism of inhibitionHIV-1 RTWild-type RTStavudine triphosphateTranscriptase inhibitorD4TD4TTPType 1WT RTMutant RTsReverse transcriptase
2005
Hoogsteen base-pairing in DNA replication?
Wang J. Hoogsteen base-pairing in DNA replication? Nature 2005, 437: e6-e7. PMID: 16163299, DOI: 10.1038/nature04199.Peer-Reviewed Original ResearchA Twisted Four-Sheeted Model for an Amyloid Fibril
Wang J, Gülich S, Bradford C, Ramirez-Alvarado M, Regan L. A Twisted Four-Sheeted Model for an Amyloid Fibril. Structure 2005, 13: 1279-1288. PMID: 16154085, DOI: 10.1016/j.str.2005.06.010.Peer-Reviewed Original Research
2001
Structure of the Replicating Complex of a Pol α Family DNA Polymerase
Franklin M, Wang J, Steitz T. Structure of the Replicating Complex of a Pol α Family DNA Polymerase. Cell 2001, 105: 657-667. PMID: 11389835, DOI: 10.1016/s0092-8674(01)00367-1.Peer-Reviewed Original ResearchConceptsAlpha familyDNA polymeraseResolution crystal structureTernary complex structureApo-protein structurePrimer-template DNAMinor groove interactionsFamily DNA polymerasesFamily polymerasesRB69 DNA polymerasePol IFidelity mechanismsPrimer 3' terminusPrimer extensionPolymeraseGroove interactionsDNA motionTerminusDNA orientationFamilyDNADegrees rotationCrystal structureComplex structureDTTP