PDB entry 6kf3

View 6kf3 on RCSB PDB site
Description: cryo-em structure of thermococcus kodakarensis rna polymerase
Deposited on 2019-07-06, released 2020-07-01
The last revision was dated 2022-03-23, with a file datestamp of 2022-03-18.
Experiment type: EM
Resolution: 3.9 Å
R-factor: N/A
AEROSPACI score: 0.12 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase subunit
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA-directed RNA polymerase subunit beta
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: DNA-directed RNA polymerase subunit A''
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: DNA-directed RNA polymerase subunit D
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: DNA-directed RNA polymerase, subunit E
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Gene: TK1699
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: DNA-directed RNA polymerase, subunit F
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Gene: TK0901
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5JI52 (0-113)
      • expression tag (114-121)
  • Chain 'H':
    Compound: DNA-directed RNA polymerase subunit H
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: DNA-directed RNA polymerase subunit K
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: DNA-directed RNA polymerase subunit L
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: DNA-directed RNA polymerase subunit N
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Chain 'P':
    Compound: DNA-directed RNA polymerase subunit P
    Species: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) [TaxId:69014]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: MG, ZN

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6kf3A (A:)
    mqsmkkvigsiefgilspqeirkmsaaeitvpdtydddgypiegglmdkrlgvidpglrc
    etcgaragecpghfghielarpvihvgfaktihrvlestcrecgrikltdeeieeymqkf
    evmgdrkgavdklikeihkkakermvcphcgapqfpikferptiywelrkdeegneykhr
    mmpsevrdrlekipdkdlpllglhpeksrpewmvltvlpvppvtmrpsitlesgiraedd
    lthklvdiirinnrlksnieagapqliiedlwdllqyhvttyinnetsgvppakhksgrp
    lktlaqrlkgkegrfrgnlsgkrvnfsartvispdpmisinevgvplavameltvpekvt
    efnyeklkqrvlngpekypganyvidpegrrirlmesnreliaekldigwtverhledgd
    vvlfnrqpslhrmsimahrvrvmpyrtfrlnlpvcppynadfdgdemnlhvpqteeaqae
    akilmevqnhiispryggpliagiqdhisggylltregayftryeveqmlmfagmdvnel
    pepdkyengeplwsgktifslllpddltiwyrnklcdepercealeklieeklipdpeev
    rklaydgfvyiqngkllsgavdkkaygredgklldiivreygverarqfldqvtkltiwv
    ithkgfttaiddedlpqeaidriheiireaeekvqrlieaykrgeleplpgktleetles
    kimavlaeardnagkvaerylgmnnhavimaktgargkilnitqmaamlgqqsirgkrly
    rgyrgrvlthfkpgdlgarargfvtnsyksgltpqeyffhamggreglvdtavrtaqsgy
    mqrrlinalqdlkvdydgtvrdptgiivqfkygedgvdpmkswqgktvdvdrvivrtllk
    mrggge
    

    Sequence, based on observed residues (ATOM records):
    >6kf3A (A:)
    kkvigsiefgilspqeirkmsaaeitvpdtydddgypiegglmdkrlgvidpglrcetcg
    aragecpghfghielarpvihvgfaktihrvlestcrecgrikltdeeieeymqkfevmg
    drkgavdklikeihkkakermvcphcgapqfpikferptiywelrkdeegneykhrmmps
    evrdrlekipdkdlpllglhpeksrpewmvltvlpvppvtmrpsitlesgiraeddlthk
    lvdiirinnrlksnieagapqliiedlwdllqyhvttyinnetsgvppakhksgrplktl
    aqrlkgkegrfrgnlsgkrvnfsartvispdpmisinevgvplavameltvpekvtefny
    eklkqrvlngpekypganyvidpegrrirlmesnreliaekldigwtverhledgdvvlf
    nrqpslhrmsimahrvrvmpyrtfrlnlpvcppynadfdgdemnlhvpqteeaqaeakil
    mevqnhiispryggpliagiqdhisggylltregayftryeveqmlmfagmdvnelpepd
    kyengeplwsgktifslllpddltiwyrnklcdepercealeklieeklipdpeevrkla
    ydgfvyiqngkllsgavdkkaygredgklldiivreygverarqfldqvtkltiwvithk
    gfttaiddedlpqeaidriheiireaeekvqrlieaykrgeleplpgktleetleskima
    vlaeardnagkvaerylgmnnhavimaktgargkilnitqmaamlgqqsirgkrlyrgyr
    grvlthfkpgdlgarargfvtnsyksgltpqeyffhamggreglvdtavrtaqsgymqrr
    linalqdlkvdydgtvrdptgiivqfkygedgvdpmkswqgktvdvdrvivrtllkmrgg
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6kf3B (B:)
    msrgvtvteptltpdelwlvmesywkekgfvrqhldsynafidhglqdvvnefgevvpdi
    pnfkvkfgkirigqpefqeaqgqrrplypmdarirnltysaplylemipvvngieqepve
    vrigelpimlkskacrlyglsdeeliklgedpkdpggyfiingservivsiedlapnktl
    verderqnkvvakvfsyrhgyralitverkkdgilyvtipnvpkpvkfvyvmralglltd
    keiveavsddpriqqvlfdnledasdistqeealdyigrlalpgqpkeyrlrraehiidn
    nllphmgvdpenrrakayylgmmalkvlelslglrgeddkdhyankrlklagdllkdlfr
    vafgqlvkdmqyqmtktyqrkgerytfeniqrfvrnsirpdvlseriehalatgswpggr
    tgvsqlldrtnymstlshlrrvtsplsrdqphfeardlhgthwgricptetpegpncglv
    knlalmsqittgiperevreylmkmgvvpieerrpapglyrvylngvligtvedgrklve
    riradrragkisdvinvalyedeevkevyinsddgrvrrplivvengkpkltrehvegik
    ngtltwsdlirmgvieyldaeeeenayvatwpwevteehthlelmpaailgipaslvpyp
    ehnaaprntygagmakqslglgwanfrirvdtrghlmhypqvplvnsrimkavgfedrpa
    gqnfvvavlsyhgynmedaviinkasierglarstffrtyeaeekrylggqkdnfevpsp
    niqgylgekyyrhldedglifpeskvegkdvlvgrtspprfieeqsslgsmvlqgrrets
    vtvrpsekgvvdkvivtetgdgtklvkvtvrdlripelgdkfasrhgqkgviglivpqed
    mpwtesgivpdlivnphgipsrmtvgqlieaiggkvasltgrrvdgtafigepeeklrke
    leelgfkhsgreimydgitgrrleadifigviyyqrlhhmvadkmharsrgpvqvltkqp
    tegraregglrfgemerdvlighgaamllierlleesdktevwvcescghlaledkrrgk
    vycpvcgederiskvemsyafkllldelkamvirpslrlkdrv
    

    Sequence, based on observed residues (ATOM records):
    >6kf3B (B:)
    eptltpdelwlvmesywkekgfvrqhldsynafidhglqdvvnefgevvpdipnfkvkfg
    kirigqpefqeaqgqrrplypmdarirnltysaplylemipvvngieqepvevrigelpi
    mlkskacrlyglsdeeliklgedpkdpggyfiingservivsiedlapnktlverderqn
    kvvakvfsyrhgyralitverkkdgilyvtipnvpkpvkfvyvmralglltdkeiveavs
    ddpriqqvlfdnledasdistqeealdyigrlalpgqpkeyrlrraehiidnnllphmgv
    dpenrrakayylgmmalkvlelslglrgeddkdhyankrlklagdllkdlfrvafgqlvk
    dmqyqmtktyqrkgerytfeniqrfvrnsirpdvlseriehalatgswpggrtgvsqlld
    rtnymstlshlrrvtsplsrdqphfeardlhgthwgricptetpegpncglvknlalmsq
    ittgiperevreylmkmgvvpieerrpapglyrvylngvligtvedgrklveriradrra
    gkisdvinvalyedeevkevyinsddgrvrrplivvengkpkltrehvegikngtltwsd
    lirmgvieyldaeeeenayvatwpwevteehthlelmpaailgipaslvpypehnaaprn
    tygagmakqslglgwanfrirvdtrghlmhypqvplvnsrimkavgfedrpagqnfvvav
    lsyhgynmedaviinkasierglarstffrtyeaeekrylggqkdnfevpspniqgylge
    kyyrhldedglifpeskvegkdvlvgrtspprfieeqsslgsmvlqgrretsvtvrpsek
    gvvdkvivtetgdgtklvkvtvrdlripelgdkfasrhgqkgviglivpqedmpwtesgi
    vpdlivnphgipsrmtvgqlieaiggkvasltgrrvdgtafigepeeklrkeleelgfkh
    sgreimydgitgrrleadifigviyyqrlhhmvadkmharsrgpvqvltkqptegrareg
    glrfgemerdvlighgaamllierlleesdktevwvcescghlaledkrrgkvycpvcge
    deriskvemsyafkllldelkamvirpslrlkdr
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6kf3C (C:)
    mvaektiksmvskaelpdnikeelyaklieynekyklkkdeiqaiidetvreyqkaliep
    geavgtvaaqsigepstqmtlntfhyagvaeinvtlglpriieivdarknpstpimtvyl
    deehrydrdkalevarriegttlenlareetidilnmeyvveidperlekagldmekvvr
    kltgsfksaefeaegytlvvrpkkvtklsdlrkiaekvkkhrlkglsgvgktiirkegde
    yviytegsnfkqvlkvpgvdptrtrtnniweiaevlgieaarnaiideivstmreqglev
    dvrhimlvadmmtldgvirpigrhgivgekasvlaraafeittqhlfaaaergevdplng
    vvenvligqpvpvgtgivklamslplrpkre
    

    Sequence, based on observed residues (ATOM records):
    >6kf3C (C:)
    vaektiksmvskaelpdnikeelyaklieynekyklkkdeiqaiidetvreyqkaliepg
    eavgtvaaqsigepstqmtlntfhyagvaeinvtlglpriieivdarknpstpimtvyld
    eehrydrdkalevarriegttlenlareetidilnmeyvveidperlekagldmekvvrk
    ltgsfksaefeaegytlvvrpkkvtklsdlrkiaekvkkhrlkglsgvgktiirkegdey
    viytegsnfkqvlkvpgvdptrtrtnniweiaevlgieaarnaiideivstmreqglevd
    vrhimlvadmmtldgvirpigrhgivgekasvlaraafeittqhlfaaaergevdplngv
    venvligqpvpvgtgivklamslplrpk
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6kf3D (D:)
    mvefkilekrpdsikfivsgvdvpfanalrrtilsevptfavdeveflendsalfdeiia
    hrlamiplttpherfsldalelddytvtlsleaegpgmvysgdlkssdgdvkpanpnipi
    vklaegqrltfnayarlgrgkdhakwqpgfvyykyltkihvskdvpdweelkelaerrgl
    pveesdeeivittikafylprkfeehmgkgireeivpgsfvftvetngelpveeivsial
    kilmrksdrfinelhklad
    

    Sequence, based on observed residues (ATOM records):
    >6kf3D (D:)
    vefkilekrpdsikfivsgvdvpfanalrrtilsevptfavdeveflendsalfdeiiah
    rlamiplttpherfsldalelddytvtlsleaegpgmvysgdlkssdgdvkpanpnipiv
    klaegqrltfnayarlgrgkdhakwqpgfvyykyltkihvskdvpdweelkelaerrglp
    veesdeeivittikafylprkfeehmgkgireeivpgsfvftvetngelpveeivsialk
    ilmrksdrfinelhkla
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6kf3E (E:)
    mykllkvkdvvripprmftmdpkeaakivlretyegiydrdegvvlaildveeisegviv
    pgdgatyheaifnvlvweprnqevvegevvemmpygafirigpmdglvhisqlmddyvvf
    deknrqfigketnrvlklgdyvrariigvsvksrvirenkinmtmrqpglgkfewiekek
    kkakeeskge
    

    Sequence, based on observed residues (ATOM records):
    >6kf3E (E:)
    mykllkvkdvvripprmftmdpkeaakivlretyegiydrdegvvlaildveeisegviv
    pgdgatyheaifnvlvweprnqevvegevvemmpygafirigpmdglvhisqlmddyvvf
    deknrqfigketnrvlklgdyvrariigvsvksrvirenkinmtmrqpglgkfewiekek
    k
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >6kf3F (F:)
    migrkkleehyitiaeakellerrhaeglaenpeepmfyearvslehaerfaklkpeqar
    elkeklmglfdwineriaaklvdilpedyldirvifakeeymptpeeaeeiikvideyrp
    le
    

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6kf3H (H:)
    maakkefnifdhvlvpehrilseeekeellkkyririsqlpqikasdpavvalgakpgdv
    ieikrksptagyyyyyrlvved
    

    Sequence, based on observed residues (ATOM records):
    >6kf3H (H:)
    efnifdhvlvpehrilseeekeellkkyririsqlpqikasdpavvalgakpgdvieikr
    ksptagyyyyyrlvve
    

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6kf3K (K:)
    mfrytrfekariigaralqiamgapvlidvpegitplqaallefekgvipitvirps
    

    Sequence, based on observed residues (ATOM records):
    >6kf3K (K:)
    frytrfekariigaralqiamgapvlidvpegitplqaallefekgvipitvirps
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records:
    >6kf3L (L:)
    mrievirreenllefylegedhtfanlltetlhenehvtfagytiehpitmarkprfkvv
    tdgkitpekaleeaaqkifdrarevleawkaaie
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records:
    >6kf3N (N:)
    mivpvrcftcgkvladkyyefkkrveagedpgkvlddlgveryccrrtllshvelidqvm
    vykvy
    

  • Chain 'P':
    Sequence, based on SEQRES records:
    >6kf3P (P:)
    matavyrcakcgkeveldlatarevrcpycgskilykprprvarrvkai
    

    Sequence, based on observed residues (ATOM records):
    >6kf3P (P:)
    yrcakcgkeveldlatarevrcpycgskilykprprvarrvkai