PDB entry 6vvt

View 6vvt on RCSB PDB site
Description: crystal structure of a mycobacterium smegmatis transcription initiation complex with rifampicin-resistant rna polymerase and antibiotic sorangicin
Deposited on 2020-02-18, released 2020-10-21
The last revision was dated 2020-12-16, with a file datestamp of 2020-12-11.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) [TaxId:246196]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) [TaxId:246196]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: DNA-directed RNA polymerase subunit beta
    Species: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) [TaxId:246196]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P60281
      • variant (446)
  • Chain 'D':
    Compound: DNA-directed RNA polymerase subunit beta'
    Species: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) [TaxId:246196]
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: DNA-directed RNA polymerase subunit omega
    Species: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) [TaxId:246196]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: RNA polymerase sigma factor SigA
    Species: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) [TaxId:246196]
    Gene: sigA, MSMEG_2758
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: RNA polymerase-binding protein RbpA
    Species: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) [TaxId:246196]
    Database cross-references and differences (RAF-indexed):
  • Chain 'O':
    Compound: DNA (31-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'P':
    Compound: DNA (26-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Heterogens: EDO, SO4, SRN, ZN, HOH

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:
    >6vvtA (A:)
    mlisqrptlseetvaenrsrfvieplepgfgytlgnslrrtllssipgaavtsiridgvl
    hefttvpgvkedvtdiilnlkglvvssdddepvtmylrkqgpgvvtagdivppagvtvhn
    pdmhiatlndkgklevelvvergrgyvpavqnkasgaeigripvdsiyspvlkvtykvea
    trveqrtdfdkliidvetknsisprdalasaggtlvelfglarelnadsehieigpspae
    adhiasfalpiddldltvrsynclkregvhtvgelvartesdlldirnfgqksidevkik
    lhqlglslkdspatfdpsevagydaatgtwtsdagydlddnqdyaeteql
    

    Sequence, based on observed residues (ATOM records):
    >6vvtA (A:)
    mlisqrptlseetvaenrsrfvieplepgfgytlgnslrrtllssipgaavtsiridgvl
    hefttvpgvkedvtdiilnlkglvvssdddepvtmylrkqgpgvvtagdivppagvtvhn
    pdmhiatlndkgklevelvvergrgyvpavqnkasgaeigripvdsiyspvlkvtykvea
    trveqrtdfdkliidvetknsisprdalasaggtlvelfgla
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6vvtB (B:)
    mlisqrptlseetvaenrsrfvieplepgfgytlgnslrrtllssipgaavtsiridgvl
    hefttvpgvkedvtdiilnlkglvvssdddepvtmylrkqgpgvvtagdivppagvtvhn
    pdmhiatlndkgklevelvvergrgyvpavqnkasgaeigripvdsiyspvlkvtykvea
    trveqrtdfdkliidvetknsisprdalasaggtlvelfglarelnadsehieigpspae
    adhiasfalpiddldltvrsynclkregvhtvgelvartesdlldirnfgqksidevkik
    lhqlglslkdspatfdpsevagydaatgtwtsdagydlddnqdyaeteql
    

    Sequence, based on observed residues (ATOM records):
    >6vvtB (B:)
    lisqrptlseetvaenrsrfvieplepgfgytlgnslrrtllssipgaavtsiridgvlh
    efttvpgvkedvtdiilnlkglvvssdddepvtmylrkqgpgvvtagdivppagvtvhnp
    dmhiatlndkgklevelvvergrgyvpaveigripvdsiyspvlkvtykveatrveqrtd
    fdkliidvetknsisprdalasaggtlvelfglarelnadsehie
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6vvtC (C:)
    mlegcilavssqsksnaitnnsvpgapnrvsfaklreplevpglldvqtdsfewlvgsdr
    wrqaaidrgeenpvggleevlaelspiedfsgsmslsfsdprfdevkasvdeckdkdmty
    aaplfvtaefinnntgeiksqtvfmgdfpmmtekgtfiingtervvvsqlvrspgvyfde
    tidkstektlhsvkvipgrgawlefdvdkrdtvgvridrkrrqpvtvllkalgwtneqiv
    erfgfseimmgtlekdttsgtdealldiyrklrpgepptkesaqtllenlffkekrydla
    rvgrykvnkklglnagkpitsstlteedvvatieylvrlhegqtsmtvpggvevpvevdd
    idhfgnrrlrtvgeliqnqirvglsrmervvrermttqdveaitpqtlinirpvvaaike
    ffgtsqlsqfmdqnnplsglthkrrllalgpgglsreraglevrdvhpshygrmcpietp
    egpnigligslsvyarvnpfgfietpyrkvengvvtdqidyltadeedrhvvaqansptd
    engrftedrvmvrkkggevefvsadqvdymdvsprqmvsvatamipflehddanralmga
    nmqrqavplvrseaplvgtgmelraaidagdvvvadktgvieevsadyitvmaddgtrqs
    yrlrkfarsnhgtcanqrpivdagqrveagqviadgpctqngemalgknllvaimpwegh
    nyedaiilsnrlveedvltsihieeheidardtklgaeeitrdipnvsdevladldergi
    vrigaevrdgdilvgkvtpkgeteltpeerllraifgekarevrdtslkvphgesgkvig
    irvfsredddelpagvnelvrvyvaqkrkisdgdklagrhgnkgvigkilpvedmpflpd
    gtpvdiilnthgvprrmnigqilethlgwvakagwnidvaagvpdwasklpeelysapad
    stvatpvfdgaqegelagllgstlpnrdgevmvdadgkstlfdgrsgepfpypvtvgymy
    ilklhhlvddkiharstgpysmitqqplggkaqfggqrfgemecwamqaygaaytlqell
    tiksddtvgrvkvyeaivkgenipepgipesfkvllkelqslclnvevlssdgaaiemrd
    gddedleraaanlginlsrnesasvedla
    

    Sequence, based on observed residues (ATOM records):
    >6vvtC (C:)
    nsvpgapnrvsfaklreplevpglldvqtdsfewlvgsdrwrqaaidrgeenpvggleev
    laelspifsdprfdevkasvdeckdkdmtyaaplfvsqtvfmgdfpmmtekgtfiingte
    rvvvsqlvrsdhfgnrrlrtvgeliqnqirvglsrmervvrermttqdveaitpqtlini
    rpvvaaikeffgtsqlsqfmdqnnplsglthkrrllalgevrdvhpshygrmcpietpeg
    pnigligslsvyarvnpfgfietpyrkvengvvtdqidyltadeedrhvvaqansptden
    grmvrkkggevdymdvsprqmvsvatamipflehddanralmganmqrqavplvrseapl
    vgtgmelraaidagdvvvadktgvieevsadyitvmaddgtrqsyrlrkfarsnhgtcan
    qrpivdagqrveagqviadgpctqngemalgknllvaimpweghnyedaiilsnrlveed
    vltsihieeheidardtklgaeeitrdipnvsdevladldergivrigaevrdgdilvgk
    vtpkgeteltpeerllraifgekarevrdtslkvphgesgkvigirvfsredddelpagv
    nelvrvyvaqkrkisdgdklagrhgnkgvigkilpvedmpflpdgtpvdiilnthgvprr
    mnigqilethlgwvakagwnidvaagvpdwasklpeelysapadstvatpvfdgaqegel
    agllgstlpnrdgevmvdadgkstlfdgrsgepfpypvtvgymyilklhhlvddkihars
    tgpysmitqqplggkaqfggqrfgemecwamqaygaaytlqelltiksddtvgrvkvyea
    ivkgenipepgipesfkvllkelqslclnvevlssdgaaiemr
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6vvtD (D:)
    mldvnffdelriglataddirnwsygevkkpetinyrtlkpekdglfcekifgptrdwec
    ycgkykrvrfkgiicercgvevtrakvrrermghielaapvthiwyfkgvpsrlgylldl
    apkdlekiiyfaayvitsvddemrhnelstleaemavekkavedqrdadlearaqklead
    laeleaegaksdvrrkvrdsgeremrqlrdraqreldrldeiwntftklapkqlivdevl
    yrelqdrygeyftgamgaesikklienfdidaeaeslrevirsgkgqkklralkrlkvva
    afqqsgnspmgmvldavpvippelrpmvqldggrfatsdlndlyrrvinrnnrlkrlidl
    gapeiivnnekrmlqesvdalfdngrrgrpvtgpgnrplkslsdllkgkqgrfrqnllgk
    rvdysgrsvivvgpqlklhqcglpklmalelfkpfvmkrlvdlnhaqniksakrmverqr
    pqvwdvleeviaehpvllnraptlhrlgiqafepqlvegkaiqlhplvceafnadfdgdq
    mavhlplsaeaqaearilmlssnnilspasgkplamprldmvtglyylttlvegatgeyq
    aatkdapeqgvysspaeaimamdrgalsvrakikvrltelrpptdleaqlfengwkpgda
    wtaettlgrvmfnellpksypfvneqmhkkvqariindlaerfpmivvaqtvdklkdagf
    ywatrsgvtvsmadvlvppqkqeilerheaeadaierkyqrgalnhterneslvkiwqda
    teevgkaleefypadnpiitivksgatgnltqtrtlagmkglvtnpkgefiprpikssfr
    egltvleyfinthgarkgladtalrtadsgyltrrlvdvsqdvivrehdceterginvtl
    aergpdgtlirdahvetsafartlatdavdangnviierghdlgdpaidallaagittvk
    vrsvltctsatgvcamcygrsmatgklvdigeavgivaaqsigepgtqltmrtfhqggvt
    ggadivgglprvqelfearvprnkapiadvagrvrleesdkffkitivpddggeevvydk
    lskrqrlrvithedgtegvlsdgdhvevgdqlmegaadphevlrvqgprevqihlvkevq
    evyraqgvsihdkhievivrqmlrrvtiidsgsteflpgslteraefeaenrrvvaegge
    paagrpvlmgitkaslatdswlsaasfqettrvltdaaincrsdklnglkenviigklip
    agtgisryrniqvqpteearaaaytipsyedqyyspdfgqatgaavplddygysdyr
    

    Sequence, based on observed residues (ATOM records):
    >6vvtD (D:)
    dvnffdelriglataddirnwsygevkkpetinyrtlkpekdglfcekifgptrdwecyc
    gkykrvrfkgiicercgvevtrakvrrermghielaapvthiwyfkgvpsrlgylldlap
    kdlekiiyfaayvitsvddemrhnelstleaemavekkavedqrdadlearaqkleadla
    eleaegaksdvrrkvrdsgeremrqlrdraqreldrldeiwntftklapkqlivdevlyr
    elqdrygeyftgamgaesikklienfdidaeaeslrevirsgkgqkklralkrlkvvaaf
    qqsgnspmgmvldavpvippelrpmvqldggrfatsdlndlyrrvinrnnrlkrlidlga
    peiivnnekrmlqesvdalfdngrrgrpvtgpgnrplkslsdllkgkqgrfrqnllgkrv
    dysgrsvivvgpqlklhqcglpklmalelfkpfvmkrlvdlnhaqniksakrmverqrpq
    vwdvleeviaehpvllnraptlhrlgiqafepqlvegkaiqlhplvceafnadfdgdqma
    vhlplsaeaqaearilmlssnnilspasgkplamprldmvtglyylttlvegatgeyqaa
    tkdapeqgvysspaeaimamdrgalsvrakikvrltelrpptdleaqlfengwkpgdawt
    aettlgrvmfnellpksypfvneqmhkkvqariindlaerfpmivvaqtvdklkdagfyw
    atrsgvtvsmadvlvppqkqeilerheaeadaierkyqrgalnhterneslvkiwqdate
    evgkaleefypadnpiitivksgatsfregltvleyfinthgarkgladtalrtadsgyl
    trrlvdvsqdvivrehdceterginvtlaergrdahvetsafartlatdavdangnviie
    rghdlgdpaidallaagittvkvrsvltctsatgvcamcygrsmatgklvdigeavgiva
    aqsigepgtqltgglprvqelfearvprnkapiadvagrvrleesdkffkitivpddgge
    evvydklskrqrlrvigvlsdgdhvevgdqlmegaadphevlrvqgprevqihlvkevqe
    vyraqgvsihdkhievivrqmlrrvtiidsteraefeaaagrpvlmgitkaslatdswls
    aasfqettrvltdaaincrsdklnglkenviigklipagtgisryrniqvqpteearaaa
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6vvtE (E:)
    mstphadaqlnaaddlgidssaasaydtplgitnppidellsrasskyalviyaakrarq
    indyynqlgdgileyvgplvepglqekplsialreihgdllehtege
    

    Sequence, based on observed residues (ATOM records):
    >6vvtE (E:)
    aydtplgitnppidellsrasskyalviyaakrarqindyynqlgdgileyvgplvepgl
    qekplsialreihgdllehteg
    

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6vvtF (F:)
    maatkaspateepvkrtatktpakkapakraaksaaakaggkapakkapakraakgtaak
    pedgvtddlevtddleaepgedldvedtdlelddldsdddtavedeeeeadaatpavata
    kaadddidepsekdkasgdfvwdeeesealrqarkdaeltasadsvraylkqigkvalln
    aeeevelakrieaglyatqklaelaekgeklpvqqrrdmqwicrdgdraknhlleanlrl
    vvslakrytgrgmafldliqegnlgliravekfdytkgykfstyatwwirqaitramadq
    artiripvhmvevinklgriqrellqdlgreptpeelakemditpekvleiqqyarepis
    ldqtigdegdsqlgdfiedseavvavdavsftllqdqlqsvletlsereagvvrlrfglt
    dgqprtldeigqvygvtrerirqiesktmsklrhpsrsqvlrdyld
    

    Sequence, based on observed residues (ATOM records):
    >6vvtF (F:)
    adsvraylkqigkvallnaeeevelakrieaglyatqklaelaekgeklpvqqrrdmqwi
    crdgdraknhlleanlrlvvslakrytgrgmafldliqegnlgliravekfdytkgykfs
    tyatwwirqaitramadqartiripvhmvevinklgriqrellqdlgreptpeelakemd
    itpekvleiqqyarepisldqtigdegdsqlgdfiedseavvavdavsftllqdqlqsvl
    etlsereagvvrlrfgltdgqprtldeigqvygvtrerirqiesktmsklrhpsrsqvlr
    dyl
    

  • Chain 'J':
    Sequence, based on SEQRES records:
    >6vvtJ (J:)
    madrvlrgsrlgavsyetdrnhdlaprqvaryrtdngeefdvpfaddaeipgtwlcrngl
    egtliegdvpepkkvkpprthwdmllerrsveeleellkerldlikakrrgtgs
    

    Sequence, based on observed residues (ATOM records):
    >6vvtJ (J:)
    prqvaryrtdngeefdvpfaddaeipgtwlcrnglegtliegdvpepkkvkpprthwdml
    lerrsveeleellkerldlikakr
    

  • Chain 'O':
    No sequence available.

  • Chain 'P':
    No sequence available.