PDB entry 2nvq

View 2nvq on RCSB PDB site
Description: RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP
Class: transcription/DNA/RNA
Keywords: transcription, mRNA, multiprotein complex, molecular machine, DNA
Deposited on 2006-11-13, released 2006-12-12
The last revision prior to the SCOP 1.75 freeze date was dated 2006-12-12, with a file datestamp of 2007-06-28.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: 0.23
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase II largest subunit
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqa1
  • Chain 'B':
    Compound: DNA-directed RNA polymerase II 140 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqb1
  • Chain 'C':
    Compound: DNA-directed RNA polymerase II 45 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqc1, d2nvqc2
  • Chain 'E':
    Compound: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqe1, d2nvqe2
  • Chain 'F':
    Compound: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqf1
  • Chain 'H':
    Compound: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqh1
  • Chain 'I':
    Compound: DNA-directed RNA polymerase II subunit 9
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqi1, d2nvqi2
  • Chain 'J':
    Compound: DNA-directed RNA polymerases I/II/III subunit 10
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqj1
  • Chain 'K':
    Compound: DNA-directed RNA polymerase II 13.6 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvqk1
  • Chain 'L':
    Compound: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2nvql1
  • 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)
    >2nvqA (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)
    >2nvqA (A:)
    gqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsid
    rnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnelm
    rqalaikdskkrfaaiwtlcktkmvcetdvpslvsrggcgntqptirkdglklvgswklr
    vlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvppppvrpsisfnesqrged
    dltfkladilkanisletlehngaphhaieeaesllqfhvatymdndiagqpqalqksgr
    pvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleldqvgvpksiaktltypevv
    tpynidrltqlvrngpnehpgakyvirdsgdridlryskragdiqlqygwkverhimdnd
    pvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynadfdgdemnlhvpqseetrae
    lsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfieldqvlnmlywvpdwdgvi
    ptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkdngmliidgqiifgvvekk
    tvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngfstgigdtiadgptmreit
    etiaeakkkvldvtkeaqanlltakhgmtlresfednvvrflneardkagrlaevnlkdl
    nnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdrtlphfskddyspeskgfv
    ensylrgltpqefffhamggreglidtavktaetgyiqrrlvkaledimvhydnttrnsl
    gnviqfiygedgmdaahiekqsldtiggsdaafekryrvdllntdhtldpsllesgseil
    gdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqnaqqtfhidhtkpsd
    ltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccllrsrlatrrvlqeyrltkq
    afdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtlntfhfagvaskkvtsgvpr
    lkeilnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydpdprs
    tvipedeeiiqlhfslqqspwllrleldraamndkdltmgqvgerikqtfkndlfviwse
    dndekliircrvvaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvk
    epewvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalykevynviasdg
    syvnyrhmallvdvmttqggltsvtrhgfnrsntgalmrcsfeetveilfeagasaeldd
    crgvsenvilgqmapigtgafdvmi
    

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • Chain 'N':
    No sequence available.

  • Chain 'R':
    No sequence available.

  • Chain 'T':
    No sequence available.