PDB entry 4q4z

View 4q4z on RCSB PDB site
Description: Thermus thermophilus RNA polymerase de novo transcription initiation complex
Class: transcription/DNA
Keywords: transcription, DNA and NTP, transcription-DNA complex
Deposited on 2014-04-15, released 2014-07-30
The last revision prior to the SCOPe 2.07 freeze date was dated 2014-10-08, with a file datestamp of 2014-10-03.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: 0.256
AEROSPACI score: 0.15 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Thermus thermophilus [TaxId:274]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4q4za1, d4q4za2
  • Chain 'B':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Thermus thermophilus [TaxId:274]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4q4zb1, d4q4zb2
  • Chain 'C':
    Compound: DNA-directed RNA polymerase subunit beta
    Species: Thermus thermophilus [TaxId:300852]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4q4zc_
  • Chain 'D':
    Compound: DNA-directed RNA polymerase subunit beta'
    Species: Thermus thermophilus [TaxId:300852]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4q4zd_
  • Chain 'E':
    Compound: DNA-directed RNA polymerase subunit omega
    Species: Thermus thermophilus [TaxId:300852]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4q4ze_
  • Chain 'F':
    Compound: RNA polymerase sigma factor SigA
    Species: Thermus thermophilus [TaxId:300852]
    Gene: sigA, TTHA0532
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4q4zf1, d4q4zf2, d4q4zf3
  • Chain 'G':
    Compound: DNA (5'-d(*cp*cp*tp*gp*cp*ap*tp*cp*cp*gp*tp*gp*ap*gp*tp*gp*cp*ap*gp*cp*cp*a)-3')
    Species:
    Gene:
  • Chain 'H':
    Compound: DNA (25-mer)
    Species:
    Gene:
  • Heterogens: ATP, ZN, MG, 2TM, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4q4zA (A:)
    mldsklkapvftvrtqgreygefvleplergfgvtlgnplrrillssipgtavtsvyied
    vlhefstipgvkedvveiilnlkelvvrflnpslqtvtlllkaegpkevkardflpvadv
    eimnpdlhiatleeggrlnmevrvdrgvgyvpaekhgikdrinaipvdavfspvrrvafq
    vedtrlgqrtdldkltlriwtdgsvtplealnqaveilrehltyfsnpqaaavaapeeak
    epeappeqeeeldlpleelglstrvlhslkeegiesvrallalnlkdlknipgigersle
    eikealekkgftlke
    

    Sequence, based on observed residues (ATOM records): (download)
    >4q4zA (A:)
    sklkapvftvrtqgreygefvleplergfgvtlgnplrrillssipgtavtsvyiedvlh
    efstipgvkedvveiilnlkelvvrflnpslqtvtlllkaegpkevkardflpvadveim
    npdlhiatleeggrlnmevrvdrgvgyvpaekhgikdrinaipvdavfspvrrvafqved
    trlgqrtdldkltlriwtdgsvtplealnqaveilrehltyfsnpqaaava
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4q4zB (B:)
    mldsklkapvftvrtqgreygefvleplergfgvtlgnplrrillssipgtavtsvyied
    vlhefstipgvkedvveiilnlkelvvrflnpslqtvtlllkaegpkevkardflpvadv
    eimnpdlhiatleeggrlnmevrvdrgvgyvpaekhgikdrinaipvdavfspvrrvafq
    vedtrlgqrtdldkltlriwtdgsvtplealnqaveilrehltyfsnpqaaavaapeeak
    epeappeqeeeldlpleelglstrvlhslkeegiesvrallalnlkdlknipgigersle
    eikealekkgftlke
    

    Sequence, based on observed residues (ATOM records): (download)
    >4q4zB (B:)
    ldsklkapvftvrtqgreygefvleplergfgvtlgnplrrillssipgtavtsvyiedv
    lhefstipgvkedvveiilnlkelvvrflnpslqtvtlllkaegpkevkardflpvadve
    imnpdlhiatleeggrlnmevrvdrgvgyvpaekhgikdrinaipvdavfspvrrvafqv
    edtrlgqrtdldkltlriwtdgsvtplealnqaveilrehltyfsnp
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4q4zC (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)
    >4q4zC (C:)
    meikrfgrireviplpplteiqvesyrralqadvppekrenvgiqaafretfpieeglvl
    dfleyrlgeppfpqdecrekdltyqaplyarlqlihkdtglikedevflghiplmtedgs
    fiingadrvivsqihrspgvyftpdparpgryiasiiplpkrgpwidlevepngvvsmkv
    nkrkfplvlllrvlgydqetlarelgaygelvqglmdesvfamrpeealirlftllrpgd
    ppkrdkavayvygliadprrydlgeagrykaeeklgirlsgrtlarfedgefkdevflpt
    lrylfaltagvpghevddidhlgnrrirtvgelmtdqfrvglarlargvrermlmgseds
    ltpaklvnsrpleaaireffsrsqlsqfkdetnplsslrhkrrisalgpggltreragfd
    vrdvhrthygricpvetpeganiglitslaayarvdelgfirtpyrrvvggvvtdevvym
    tateedrytiaqantplegnriaaervvarrkgepvivspeevefmdvspkqvfsvntnl
    ipflehddanralmgsnmqtqavpliraqapvvmtgleervvrdslaalyaeedgevakv
    dgnrivvryedgrlveyplrrfyrsnqgtaldqrprvvvgqrvrkgdlladgpasengfl
    algqnvlvaimpfdgynfedaiviseellkrdfytsihieryeieardtklgperitrdi
    phlseaalrdldeegvvrigaevkpgdilvgrtsfkgeseptpeerllrsifgekardvk
    dtslrvppgeggivvrtvrlrrgdpgvelkpgvrevvrvyvaqkrklqvgdklanrhgnk
    gvvakilpvedmphlpdgtpvdvilnplgvpsrmnlgqilethlglagyflgqryispif
    dgakepeikellaqafevyfgkrkgegfgvdkrevevlrraeklglvtpgktpeeqlkel
    flqgkvvlydgrtgepiegpivvgqmfimklyhmvedkmharstgpyslitqqplggkaq
    fggqrfgemevwaleaygaahtlqemltlksddiegrnaayeaiikgedvpepsvpesfr
    vlvkelqalaldvqtldekdnpvdifeglask
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4q4zD (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)
    >4q4zD (D:)
    kevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecacgk
    ykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsate
    leqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvkdg
    eevvkgqelapgvvsrldgvalyrfprrvrveyvkkeraglrlplaawvekeaykpgeil
    aelpepylfraeeegvvelkeleegaflvlrredepvatyflpvgmtplvvhgeivekgq
    plaeakgllrmprqvraaqveaeeegetvyltlflewtepkdyrvqphmnvvvpegarve
    agdkivaaidpeeeviaeaegvvhlhepasilvvkarvypfeddvevstgdrvapgdvla
    dggkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekelleemk
    hpsrarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdlnd
    lyrrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrplrs
    ltdilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkkme
    ekgiapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvlve
    gqsiqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplakps
    rdiilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlkyv
    fanpdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweliql
    dvpqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeekkq
    yleeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnplyv
    maqsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkgga
    dtalrtadsgyltrklvdvtheivvreadcgttnyisvplfqpdevtrslrlrkradiea
    glygrvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygvcq
    kcygydlsmarpvsigeavgivaaqsigepgtqltmrtfhtggitqglprvielfearrp
    kakaviseidgvvrieeteeklsvfvesegfskeyklpkearllvkdgdyveagqpltrg
    aidphqlleakgpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyvevtdpgdsr
    llegqvlekwdvealnerliaegktpvawkpllmgvtksalstkswlsaasfqntthvlt
    eaaiagkkdeliglkenvilgrlipagtgsdfvrftqvvdqktlkaieearkea
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4q4zE (E:)
    maepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpna
    vtwamkelltgrlvfgenlvpedrlqkemerlypveree
    

    Sequence, based on observed residues (ATOM records): (download)
    >4q4zE (E:)
    aepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpnav
    twamkelltgrlvfgenlvpedrlqkemerlypv
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4q4zF (F:)
    mkkskrknaqaqeaqetevlvqeeaeelpefpegepdpdledpdltleddlldlpeegeg
    ldleeeeedlpipkistsdpvrqylheigqvplltleeevelarkveegmeaikklseit
    gldpdlirevvrakilgsarvrhipglketldpktveeidqklkslpkehkrylhiareg
    eaarqhlieanlrlvvsiakkytgrglsfldliqegnqgliravekfeykrrfkfstyat
    wwirqainraiadqartiripvhmvetinklsrtarqlqqelgreptyeeiaeamgpgwd
    akrveetlkiaqepvsletpigdekdsfygdfipdehlpspvdaatqsllseelekalsk
    lsereamvlklrkglidgrehtleevgaffgvtrerirqienkalrklkyhesrtrklrd
    fld
    

    Sequence, based on observed residues (ATOM records): (download)
    >4q4zF (F:)
    sdpvrqylheigqvplltleeevelarkveegmeaikklseitgldpdlirevvrakilg
    sarvrhipglketldpktveeidqklkslpkehkrylhiaregeaarqhlieanlrlvvs
    iakkytgrglsfldliqegnqgliravekfeykrrfkfstyatwwirqainraiadqart
    iripvhmvetinklsrtarqlqqelgreptyeeiaeamgpgwdakrveetlkiaqepvsl
    etpigdekdsfygdfipdehlpspvdaatqsllseelekalsklsereamvlklrkglid
    grehtleevgaffgvtrerirqienkalrklkyhesrtrklrdfld
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.