PDB entry 2nvx

View 2nvx on RCSB PDB site
Description: RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP
Class: transcription,transferase/DNA-RNA hybrid
Keywords: transcription, mRNA, multiprotein complex, molecular machine, DNA, transcription,transferase/DNA-RNA hybrid complex
Deposited on 2006-11-13, released 2006-12-19
The last revision prior to the SCOPe 2.01 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 3.6 Å
R-factor: 0.286
AEROSPACI score: 0.07 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase II largest subunit
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxa1
  • Chain 'B':
    Compound: DNA-directed RNA polymerase II 140 kDa polypeptide
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxb1
  • Chain 'C':
    Compound: DNA-directed RNA polymerase II 45 kDa polypeptide
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxc1, d2nvxc2
  • Chain 'E':
    Compound: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxe1, d2nvxe2
  • Chain 'F':
    Compound: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxf1
  • Chain 'H':
    Compound: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxh1
  • Chain 'I':
    Compound: DNA-directed RNA polymerase II subunit 9
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxi1, d2nvxi2
  • Chain 'J':
    Compound: DNA-directed RNA polymerases I/II/III subunit 10
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxj1
  • Chain 'K':
    Compound: DNA-directed RNA polymerase II 13.6 kDa polypeptide
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxk1
  • Chain 'L':
    Compound: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2nvxl1
  • Chain 'N':
    Compound: 5'-d(*cp*tp*gp*cp*tp*tp*ap*tp*cp*gp*gp*tp*ap*g)-3'
  • Chain 'R':
    Compound: 5'-r(*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3'
  • Chain 'T':
    Compound: 28-MER DNA template strand
  • Heterogens: ZN, MG, DUT

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2nvxA (A:)
    mvgqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgs
    idrnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehne
    lmrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglk
    lvgswkkdratgdadepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclp
    vppppvrpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhv
    atymdndiagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnle
    ldqvgvpksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskr
    agdiqlqygwkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspyna
    dfdgdemnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtf
    ieldqvlnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllsp
    kdngmliidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhn
    gfstgigdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvr
    flneardkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfv
    drtlphfskddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrr
    lvkaledimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvd
    llntdhtldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvni
    rriiqnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfcc
    llrsrlatrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmt
    lntfhfagvaskkvtsgvprlkeilnvaknmktpsltvylepghaadqeqaklirsaieh
    ttlksvtiaseiyydpdprstvipedeeiiqlhfslldeeaeqsfdqqspwllrleldra
    amndkdltmgqvgerikqtfkndlfviwsedndekliircrvvrpksldaeteaeedhml
    kkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvp
    gidptriytnsfidimevlgieagraalykevynviasdgsyvnyrhmallvdvmttqgg
    ltsvtrhgfnrsntgalmrcsfeetveilfeagasaelddcrgvsenvilgqmapigtga
    fdvmideeslvkympeqkiteiedgqdggvtpysnesglvnadldvkdelmfsplvdsgs
    ndamaggftayggadygeatspfgaygeaptspgfgvsspgfsptsptysptspayspts
    psysptspsysptspsysptspsysptspsysptspsysptspsysptspsysptspsys
    ptspsysptspsysptspsysptspsysptspsysptspaysptspsysptspsysptsp
    sysptspsysptspnysptspsysptspgyspgspayspkqdeqkhnenensr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxA (A:)
    gqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsid
    rnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnelm
    rqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglklv
    gswklrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvppppvrpsisfne
    sqrgeddltfkladilkanisletlehngaphhaieeaesllqfhvatymdndiagqpqa
    lqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleldqvgvpksiaktl
    typevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskragdiqlqygwkver
    himdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynadfdgdemnlhvpqs
    eetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfieldqvlnmlywvp
    dwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkdngmliidgqiif
    gvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngfstgigdtiadgp
    tmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvrflneardkagrlae
    vnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdrtlphfskddysp
    eskgfvensylrgltpqefffhamggreglidtavktaetgyiqrrlvkaledimvhydn
    ttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvdllntdhtldpslle
    sgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqnaqqtfhid
    htkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccllrsrlatrrvlqe
    yrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtlkkvtsgvprlkei
    lnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydpdprstvip
    edeeiiqlhfslqqspwllrleldraamndkdltmgqvgerikqtfkndlfviwsednde
    kliircrvvraeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvkepe
    wvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalykevynviasdgsyv
    nyrhmallvdvmttqggltsvtrhgfnrsntgalmrcsfeetveilfeagasaelddcrg
    vsenvilgqmapigtgafdvmi
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2nvxB (B:)
    msdlansekyydedpygfedesapitaedswavisaffrekglvsqqldsfnqfvdytlq
    diicedstlileqlaqhttesdnisrkyeisfgkiyvtkpmvnesdgvthalypqearlr
    nltyssglfvdvkkrtyeaidvpgrelkyeliaeeseddsesgkvfigrlpimlrskncy
    lseatesdlyklkecpfdmggyfiingsekvliaqersagnivqvfkkaapspishvaei
    rsalekgsrfistlqvklygregssartikatlpyikqdipiviifralgiipdgeileh
    icydvndwqmlemlkpcvedgfviqdretaldfigrrgtalgikkekriqyakdilqkef
    lphitqlegfesrkafflgyminrlllcaldrkdqddrdhfgkkrldlagpllaqlfktl
    fkkltkdifrymqrtveeahdfnmklainaktitsglkyalatgnwgeqkkamssragvs
    qvlnrytysstlshlrrtntpigrdgklakprqlhnthwglvcpaetpegqacglvknls
    lmscisvgtdpmpiitflsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetl
    rtlrrkgdinpevsmirdirekelkiftdagrvyrplfiveddeslghkelkvrkghiak
    lmateyqdieggfedveeytwssllneglveyidaeeeesiliamqpedlepaeaneend
    ldvdpakrirvshhattfthceihpsmilgvaasiipfpdhnqsprntyqsamgkqamgv
    fltnynvrmdtmanilyypqkplgttrameylkfrelpagqnaivaiacysgynqedsmi
    mnqssidrglfrslffrsymdqekkygmsitetfekpqrtntlrmkhgtydkldddglia
    pgvrvsgedviigkttpispdeeelgqrtayhskrdastplrstengivdqvlvttnqdg
    lkfvkvrvrttkipqigdkfasrhgqkgtigityrredmpftaegivpdliinphaipsr
    mtvahliecllskvaalsgnegdaspftditvegiskllrehgyqsrgfevmynghtgkk
    lmaqiffgptyyqrlrhmvddkiharargpmqvltrqpvegrsrdgglrfgemerdcmia
    hgaasflkerlmeasdafrvhicgicglmtviaklnhnqfeckgcdnkidiyqihipyaa
    kllfqelmamnitprlytdrsrdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxB (B:)
    desapitaedswavisaffrekglvsqqldsfnqfvdytlqdiicedstliyeisfgkiy
    vtkpmvnesdgvthalypqearlrnltyssglfvdvkkkvfigrlpimlrskncylseat
    esdlyklkecpfdmggyfiingsekvliaqersagnivqvfkkaapspishvaeirsale
    kgsrfistlqvklygregssartikatlpyikqdipiviifralgiipdgeilehicydv
    ndwqmlemlkpcvedgfviqdretaldfigrrgtalgikkekriqyakdilqkeflphit
    qlegfesrkafflgyminrlllcaldrkdqddrdhfgkkrldlagpllaqlfktlfkklt
    kdifrymqrtvelainaktitsglkyalatgnwgeqkkamssragvsqvlnrytysstls
    hlrrtntpiakprqlhnthwglvcpaetpegqacglvknlslmscisvgtdpmpiitfls
    ewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkgdinpevsmirdi
    rekelkiftdagrvyrplfiveddeslghkelkvrkghiaklmateyqdeeytwssllne
    glveyidaeeeesiliamqpedlepaedvdpakrirvshhattfthceihpsmilgvaas
    iipfpdhnqsprntyqsamgkqamgvfltnynvrmdtmanilyypqkplgttrameylkf
    relpagqnaivaiacysgynqedsmimnqssidrglfrslffrsymdqekksitetfekp
    qrtntlrmkhgtydkldddgliapgvrvsgedviigkttpispdskrdastplrstengi
    vdqvlvttnqdglkfvkvrvrttkipqigdkfasrhgqkgtigityrredmpftaegivp
    dliinphaipsrmtvahliecllskvaalsgnegdaspftditvegiskllrehgyqsrg
    fevmynghtgkklmaqiffgptyyqrlrhmvddkiharargpmqvltrqpvegrsrdggl
    rfgemerdcmiahgaasflkerlmeasdafrvhicgicglmtviaklnhnqfeckgcdnk
    idiyqihipyaakllfqelmamnitprlytdrsr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2nvxC (C:)
    mseegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvlad
    efiahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlvi
    vsnlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefey
    dpwnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipv
    dqvvvrgidtlqkkvasillaltqmdqdkvnfasgdnntasnmlgsnedvmmtgaeqdpy
    snasqmgntgsggydnaw
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxC (C:)
    eegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvladef
    iahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlvivs
    nlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefeydp
    wnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipvdq
    vvvrgidtlqkkvasillaltqmdqd
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2nvxE (E:)
    mdqenernisrlwrafrtvkemvkdrgyfitqeevelpledfkakycdsmgrpqrkmmsf
    qanpteesiskfpdmgslwvefcdepsvgvktmktfvihiqeknfqtgifvyqnnitpsa
    mklvpsippatietfneaalvvnithhelvpkhirlssdekrellkryrlkesqlpriqr
    adpvalylglkrgevvkiirksetsgryasyricm
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxE (E:)
    dqenernisrlwrafrtvkemvkdrgyfitqeevelpledfkakycdsmgrpqrkmmsfq
    anpteesiskfpdmgslwvefcdepsvgvktmktfvihiqeknfqtgifvyqnnitpsam
    klvpsippatietfneaalvvnithhelvpkhirlssdekrellkryrlkesqlpriqra
    dpvalylglkrgevvkiirksetsgryasyricm
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2nvxF (F:)
    msdyeeafndgnenfedfdvehfsdeetyeekpqfkdgettdangktivtggngpedfqq
    heqirrktlkekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplri
    amkelaekkiplvirrylpdgsfedwsveelivdl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxF (F:)
    tlkekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplriamkelae
    kkiplvirrylpdgsfedwsveelivdl
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >2nvxH (H:)
    msntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtia
    sslnledtpandssatrswrppqagdrsladdydyvmygtaykfeevskdliavyysfgg
    llmrlegnyrnlnnlkqenayllirr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxH (H:)
    msntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtia
    ssltrswrppqagdrsladdydyvmygtaykfeevskdliavyysfggllmrlegnyrnl
    nnlkqenayllirr
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >2nvxI (I:)
    mttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvq
    digsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknkrtq
    fs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxI (I:)
    ttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvqd
    igsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknkrtq
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >2nvxJ (J:)
    mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
    lrynplekrd
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxJ (J:)
    mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
    lrynp
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >2nvxK (K:)
    mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
    ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtlaaddaf
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxK (K:)
    mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
    ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtl
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >2nvxL (L:)
    msregfqiptnldaaaagtsqartatlkyicaecssklslsrtdavrckdcghrillkar
    tkrlvqfear
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvxL (L:)
    atlkyicaecssklslsrtdavrckdcghrillkartkrlvqfear
    

  • Chain 'N':
    No sequence available.

  • Chain 'R':
    No sequence available.

  • Chain 'T':
    No sequence available.