PDB entry 4oio

View 4oio on RCSB PDB site
Description: Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation
Class: transcription, transferase
Keywords: de novo transcription initiation, substrate complex, transcription initiation, i site, i+1 site, RNA polymerase, DNA/RNA/NTP binding, polymerization of ribonucleotides, nucleoid, TRANSCRIPTION, TRANSFERASE
Deposited on 2014-01-20, released 2014-05-07
The last revision prior to the SCOPe 2.04 freeze date was dated 2014-05-07, with a file datestamp of 2014-05-02.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: 0.206
AEROSPACI score: 0.17 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: DNA-directed RNA polymerase subunit beta
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d4oioc_
  • Chain 'D':
    Compound: DNA-directed RNA polymerase subunit beta'
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d4oiod_
  • Chain 'E':
    Compound: DNA-directed RNA polymerase subunit omega
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d4oioe_
  • Chain 'F':
    Compound: DNA directed RNA polymerase sigma factor A
    Species: Thermus thermophilus [TaxId:300852]
    Gene: rpoD, TTHA0532
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d4oiof1, d4oiof2, d4oiof3
  • Chain 'G':
    Compound: 5'-d(*cp*cp*tp*gp*cp*ap*tp*cp*cp*gp*tp*gp*ap*gp*tp*cp*gp*ap*gp*gp*g)-3'
  • Chain 'H':
    Compound: 5'-d(*tp*ap*tp*ap*ap*tp*gp*gp*gp*ap*gp*cp*tp*gp*tp*cp*ap*cp*gp*gp*ap*tp*gp*cp*ap*gp*g)-3'
  • Heterogens: ZN, MG, ATP, 2TM, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4oioC (C:)
    meikrfgrireviplpplteiqvesyrralqadvppekrenvgiqaafretfpieeedkg
    kgglvldfleyrlgeppfpqdecrekdltyqaplyarlqlihkdtglikedevflghipl
    mtedgsfiingadrvivsqihrspgvyftpdparpgryiasiiplpkrgpwidlevepng
    vvsmkvnkrkfplvlllrvlgydqetlarelgaygelvqglmdesvfamrpeealirlft
    llrpgdppkrdkavayvygliadprrydlgeagrykaeeklgirlsgrtlarfedgefkd
    evflptlrylfaltagvpghevddidhlgnrrirtvgelmtdqfrvglarlargvrerml
    mgsedsltpaklvnsrpleaaireffsrsqlsqfkdetnplsslrhkrrisalgpggltr
    eragfdvrdvhrthygricpvetpeganiglitslaayarvdelgfirtpyrrvvggvvt
    devvymtateedrytiaqantplegnriaaervvarrkgepvivspeevefmdvspkqvf
    svntnlipflehddanralmgsnmqtqavpliraqapvvmtgleervvrdslaalyaeed
    gevakvdgnrivvryedgrlveyplrrfyrsnqgtaldqrprvvvgqrvrkgdlladgpa
    sengflalgqnvlvaimpfdgynfedaiviseellkrdfytsihieryeieardtklgpe
    ritrdiphlseaalrdldeegvvrigaevkpgdilvgrtsfkgeseptpeerllrsifge
    kardvkdtslrvppgeggivvrtvrlrrgdpgvelkpgvrevvrvyvaqkrklqvgdkla
    nrhgnkgvvakilpvedmphlpdgtpvdvilnplgvpsrmnlgqilethlglagyflgqr
    yispifdgakepeikellaqafevyfgkrkgegfgvdkrevevlrraeklglvtpgktpe
    eqlkelflqgkvvlydgrtgepiegpivvgqmfimklyhmvedkmharstgpyslitqqp
    lggkaqfggqrfgemevwaleaygaahtlqemltlksddiegrnaayeaiikgedvpeps
    vpesfrvlvkelqalaldvqtldekdnpvdifeglaskr
    

    Sequence, based on observed residues (ATOM records): (download)
    >4oioC (C:)
    meikrfgrireviplpplteiqvesyrralqadvppekrenvgiqaafretfpieelvld
    fleyrlgeppfpqdecrekdltyqaplyarlqlihkdtglikedevflghiplmtedgsf
    iingadrvivsqihrspgvyftpdparpgryiasiiplpkrgpwidlevepngvvsmkvn
    krkfplvlllrvlgydqetlarelgaygelvqglmdesvfamrpeealirlftllrpgdp
    pkrdkavayvygliadprrydlgeagrykaeeklgirlsgrtlarfedgefkdevflptl
    rylfaltagvpghevddidhlgnrrirtvgelmtdqfrvglarlargvrermlmgsedsl
    tpaklvnsrpleaaireffsrsqlsqfkdetnplsslrhkrrisalgpggltreragfdv
    rdvhrthygricpvetpeganiglitslaayarvdelgfirtpyrrvvggvvtdevvymt
    ateedrytiaqantplegnriaaervvarrkgepvivspeevefmdvspkqvfsvntnli
    pflehddanralmgsnmqtqavpliraqapvvmtgleervvrdslaalyaeedgevakvd
    gnrivvryedgrlveyplrrfyrsnqgtaldqrprvvvgqrvrkgdlladgpasengfla
    lgqnvlvaimpfdgynfedaiviseellkrdfytsihieryeieardtklgperitrdip
    hlseaalrdldeegvvrigaevkpgdilvgrtsfkgeseptpeerllrsifgekardvkd
    tslrvppgeggivvrtvrlrrgdpgvelkpgvrevvrvyvaqkrklqvgdklanrhgnkg
    vvakilpvedmphlpdgtpvdvilnplgvpsrmnlgqilethlglagyflgqryispifd
    gakepeikellaqafevyfgkrkgegfgvdkrevevlrraeklglvtpgktpeeqlkelf
    lqgkvvlydgrtgepiegpivvgqmfimklyhmvedkmharstgpyslitqqplggkaqf
    ggqrfgemevwaleaygaahtlqemltlksddiegrnaayeaiikgedvpepsvpesfrv
    lvkelqalaldvqtldekdnpvdifeglask
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4oioD (D:)
    mkkevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecac
    gkykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsa
    teleqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvk
    dgeevvkgqelapgvvsrldgvalyrfprrvrveyvkkeraglrlplaawvekeaykpge
    ilaelpepylfraeeegvvelkeleegaflvlrredepvatyflpvgmtplvvhgeivek
    gqplaeakgllrmprqvraaqveaeeegetvyltlflewtepkdyrvqphmnvvvpegar
    veagdkivaaidpeeeviaeaegvvhlhepasilvvkarvypfeddvevstgdrvapgdv
    ladggkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekellee
    mkhpsrarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdl
    ndlyrrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrpl
    rsltdilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkk
    meekgiapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvl
    vegqsiqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplak
    psrdiilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlk
    yvfanpdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweli
    qldvpqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeek
    kqyleeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnpl
    yvmaqsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkg
    gadtalrtadsgyltrklvdvtheivvreadcgttnyisvplfqpdevtrslrlrkradi
    eaglygrvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygv
    cqkcygydlsmarpvsigeavgivaaqsigepgtqltmrtfhtggvagaaditqglprvi
    elfearrpkakaviseidgvvrieeteeklsvfvesegfskeyklpkearllvkdgdyve
    agqpltrgaidphqlleakgpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyve
    vtdpgdsrllegqvlekwdvealnerliaegktpvawkpllmgvtksalstkswlsaasf
    qntthvlteaaiagkkdeliglkenvilgrlipagtgsdfvrftqvvdqktlkaieeark
    eaveakerpaarrgvkreqpgkqa
    

    Sequence, based on observed residues (ATOM records): (download)
    >4oioD (D:)
    kevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecacgk
    ykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsate
    leqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvkdg
    eevvkgqelapgvvsrldgvalyrfprrvrveyvkkeraglrlplaawvekeaykpgeil
    aelpepylfraeeegvvelkeleegaflvlrredepvatyflpvgmtplvvhgeivekgq
    plaeakgllrmprqvraaqveaeeegetvyltlflewtepkdyrvqphmnvvvpegarve
    agdkivaaidpeeeviaeaegvvhlhepasilvvkarvypfeddvevstgdrvapgdvla
    dggkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekelleemk
    hpsrarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdlnd
    lyrrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrplrs
    ltdilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkkme
    ekgiapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvlve
    gqsiqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplakps
    rdiilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlkyv
    fanpdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweliql
    dvpqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeekkq
    yleeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnplyv
    maqsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkgga
    dtalrtadsgyltrklvdvtheivvreadcgttnyisvplfqptrslrlrkradieagly
    grvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygvcqkcy
    gydlsmarpvsigeavgivaaqsigepgtqltmrqglprvielfearrpkakaviseidg
    vvrieeteeklsvfvesegfskeyklpkearllvkdgdyveagqpltrgaidphqlleak
    gpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyvevtdpgdsrllegqvlekwd
    vealnerliaegktpvawkpllmgvtksalstkswlsaasfqntthvlteaaiagkkdel
    iglkenvilgrlipagtgsdfvrftqvvdqktlkaieea
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4oioE (E:)
    maepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpna
    vtwamkelltgrlvfgenlvpedrlqkemerlypveree
    

    Sequence, based on observed residues (ATOM records): (download)
    >4oioE (E:)
    aepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpnav
    twamkelltgrlvfgenlvpedrlqkemerlypv
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4oioF (F:)
    mgsshhhhhhssglvprgshmkkskrknaqaqeaqetevlvqeeaeelpefpegepdpdl
    edpdltleddlldlpeegegldleeeeedlpipkistsdpvrqylheigqvplltleeev
    elarkveegmeaikklseitgldpdlirevvrakilgsarvrhipglketldpktveeid
    qklkslpkehkrylhiaregeaarqhlieanlrlvvsiakkytgrglsfldliqegnqgl
    iravekfeykrrfkfstyatwwirqainraiadqartiripvhmvetinklsrtarqlqq
    elgreptyeeiaeamgpgwdakrveetlkiaqepvsletpigdekdsfygdfipdehlps
    pvdaatqsllseelekalsklsereamvlklrkglidgrehtleevgaffgvtrerirqi
    enkalrklkyhesrtrklrdfld
    

    Sequence, based on observed residues (ATOM records): (download)
    >4oioF (F:)
    sdpvrqylheigqvplltleeevelarkveegmeaikklseitgldpdlirevvrakilg
    sarvrhipglketldpktveeidqklkslpkehkrylhiaregeaarqhlieanlrlvvs
    iakkytgrglsfldliqegnqgliravekfeykrrfkfstyatwwirqainraiadqart
    iripvhmvetinklsrtarqlqqelgreptyeeiaeamgpgwdakrveetlkiaqepvsl
    etpigdekdsfygdfipdehlpspvdaatqsllseelekalsklsereamvlklrkglid
    grehtleevgaffgvtrerirqienkalrklkyhesrtrklrdf
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.