PDB entry 2nvt

View 2nvt on RCSB PDB site
Description: RNA Polymerase II Elongation Complex in 150 mM Mg+2 with GMPCPP
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 2006-12-12
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 3.36 Å
R-factor: 0.232
AEROSPACI score: 0.1 (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 2.06: d2nvta1
  • 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 2.06: d2nvtb1
  • 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 2.06: d2nvtc1, d2nvtc2
  • 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 2.06: d2nvte1, d2nvte2
  • 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 2.06: d2nvtf1
  • 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 2.06: d2nvth1
  • 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 2.06: d2nvti1, d2nvti2
  • 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 2.06: d2nvtj1
  • 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 2.06: d2nvtk1
  • 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 2.06: d2nvtl1
  • Chain 'N':
    Compound: 5'-d(*gp*tp*ap*cp*tp*tp*g)-3'
  • Chain 'R':
    Compound: 5'-r(*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3'
  • Chain 'T':
    Compound: 5'-d(p*cp*ap*ap*gp*tp*ap*cp*tp*tp*ap*cp*gp*cp*cp*tp*gp*gp*tp*cp*tp*t)-3'
  • Heterogens: ZN, MG, G2P

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2nvtA (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)
    >2nvtA (A:)
    gqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsid
    rnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnelm
    rqalaikdskkrfaaiwtlcktkmvcetdvpslvsrggcgntqptirkdglklvgswklr
    vlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvppppvrpsisfnesqrged
    dltfkladilkanisletlehngaphhaieeaesllqfhvatymdndiagqpqalqksgr
    pvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleldqvgvpksiaktltypevv
    tpynidrltqlvrngpnehpgakyvirdsgdridlryskragdiqlqygwkverhimdnd
    pvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynadfdgdemnlhvpqseetrae
    lsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfieldqvlnmlywvpdwdgvi
    ptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkdngmliidgqiifgvvekk
    tvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngfstgigdtiadgptmreit
    etiaeakkkvldvtkeaqanlltakhgmtlresfednvvrflneardkagrlaevnlkdl
    nnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdrtlphfskddyspeskgfv
    ensylrgltpqefffhamggreglidtavktaetgyiqrrlvkaledimvhydnttrnsl
    gnviqfiygedgmdaahiekqsldtiggsdaafekryrvdllntdhtldpsllesgseil
    gdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqnaqqtfhidhtkpsd
    ltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccllrsrlatrrvlqeyrltkq
    afdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtlntfhfagvaskkvtsgvpr
    lkeilnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydpdprs
    tvipedeeiiqlhfslqqspwllrleldraamndkdltmgqvgerikqtfkndlfviwse
    dndekliircrvvaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvk
    epewvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalykevynviasdg
    syvnyrhmallvdvmttqggltsvtrhgfnrsntgalmrcsfeetveilfeagasaeldd
    crgvsenvilgqmapigtgafdvmideeslv
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2nvtB (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)
    >2nvtB (B:)
    desapitaedswavisaffrekglvsqqldsfnqfvdytlqdiicedstlieisfgkiyv
    tkpmvnesdgvthalypqearlrnltyssglfvdvkkrtyeaidkvfigrlpimlrsknc
    ylseatesdlyklkecpfdmggyfiingsekvliaqersagnivqvfkkaapspishvae
    irsalekgsrfistlqvklygregssartikatlpyikqdipiviifralgiipdgeile
    hicydvndwqmlemlkpcvedgfviqdretaldfigkekriqyakdilqkeflphitqle
    gfesrkafflgyminrlllcaldrkdqddrdhfgkkrldlagpllaqlfktlfkkltkdi
    frymqrtvelainaktitsglkyalatgnwgeqkkamssragvsqvlnrytysstlshlr
    rtntpiakprqlhnthwglvcpaetpegqacglvknlslmscisvgtdpmpiitflsewg
    mepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkgdinpevsmirdirek
    elkiftdagrvyrplfiveddeslghkelkvrkghiaklmateyqdeytwssllneglve
    yidaeeeesiliamqpedlepaeadvdpakrirvshhattfthceihpsmilgvaasiip
    fpdhnqsprntyqsamgkqamgvfltnynvrmdtmanilyypqkplgttrameylkfrel
    pagqnaivaiacysgynqedsmimnqssidrglfrslffrsymdqekkygmsitetfekp
    qrtntlrmkhgtydkldddgliapgvrvsgedviigkttpisskrdastplrstengivd
    qvlvttnqdglkfvkvrvrttkipqigdkfasrhgqkgtigityrredmpftaegivpdl
    iinphaipsrmtvahliecllskvaalsgnegdaspftditvegiskllrehgyqsrgfe
    vmynghtgkklmaqiffgptyyqrlrhmvddkiharargpmqvltrqpvegrsrdgglrf
    gemerdcmiahgaasflkerlmeasdafrvhicgicglmtviaklnhnqfeckgcdnkid
    iyqihipyaakllfqelmamnitprlytdrsrdf
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >2nvtC (C:)
    seegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvlade
    fiahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlviv
    snlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefeyd
    pwnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipvd
    qvvvrgidtlqkkvasillaltqmdqd
    

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

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >2nvtF (F:)
    ekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplriamkelaekki
    plvirrylpdgsfedwsveelivdl
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >2nvtH (H:)
    sntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtias
    sltrswrppqagdrsladdydyvmygtaykfeevskdliavyysfggllmrlegnyrnln
    nlkqenayllirr
    

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

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

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

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

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

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

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

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

  • Chain 'N':
    No sequence available.

  • Chain 'R':
    No sequence available.

  • Chain 'T':
    No sequence available.