6KF9

Cryo-EM structure of Thermococcus kodakarensis RNA polymerase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Cryo-EM structure of Thermococcus kodakarensis RNA polymerase

Jun, S.-H.Hyun, J.Jeong, H.Cha, J.S.Kim, H.Bartlett, M.S.Cho, H.-S.Murakami, K.S.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitA906Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1082
EC: 2.7.7.6
Find proteins for Q5JE33 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Go to UniProtKB:  Q5JE33
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit NN65Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoNTK1499
EC: 2.7.7.6
Find proteins for Q5JJC9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit PP49Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoPTK0616
EC: 2.7.7.6
Find proteins for Q5JDM8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor EG185Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK2024tfe
Find proteins for Q5JDD5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaB1123Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1083
EC: 2.7.7.6
Find proteins for Q5JE32 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit A''C391Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoA2TK1081
EC: 2.7.7.6
Find proteins for Q5JE34 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit DD259Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoDTK1503
EC: 2.7.7.6
Find proteins for Q5JJF4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, subunit EE190Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1699
Find proteins for Q5JIY4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, subunit FF122Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0901
Find proteins for Q5JI52 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit HH82Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoHTK1084
EC: 2.7.7.6
Find proteins for Q5JE31 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit KK57Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoKTK1498
EC: 2.7.7.6
Find proteins for Q5JJD0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit LL94Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoLTK1167
EC: 2.7.7.6
Find proteins for Q5JE88 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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  • Reference Sequence
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  • Entity ID: 13
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*CP*GP*GP*TP*AP*AP*TP*CP*AP*CP*GP*CP*TP*CP*C)-3')X16Thermococcus kodakarensis KOD1
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    Entity ID: 14
    MoleculeChainsLengthOrganismImage
    DNA (27-MER)Y27Thermococcus kodakarensis KOD1
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

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    A, B, G, N, P
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    A
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.79 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Ministry of Education (Korea)Korea, Republic Of2015R1D1A1A01059097
    Ministry of Science, ICT and Future PlanningKorea, Republic OfNRF-2017M3A9F6029755
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM131860
    National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesR15 GM083306

    Revision History 

    • Version 1.0: 2020-07-01
      Type: Initial release