PDB entry 1y1w

View 1y1w on RCSB PDB site
Description: Complete RNA Polymerase II elongation complex
Class: transferase/DNA/RNA
Keywords: RNA Polymerase II, transcription bubble, transcription, elongation complex
Deposited on 2004-11-19, released 2005-01-04
The last revision prior to the SCOP 1.75 freeze date was dated 2005-01-04, with a file datestamp of 2007-06-04.
Experiment type: XRAY
Resolution: 4 Å
R-factor: 0.253
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
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1y1wa_
  • 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: d1y1wb_
  • 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: d1y1wc_
  • Chain 'D':
    Compound: DNA-directed RNA polymerase II 32 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1y1wd_
  • 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: d1y1we_
  • 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: d1y1wf_
  • Chain 'G':
    Compound: DNA-directed RNA polymerase II 19 kDa polypeptide
    Species: Saccharomyces cerevisiae
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1y1wg_
  • 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: d1y1wh_
  • 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: d1y1wi_
  • 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: d1y1wj_
  • 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: d1y1wk_
  • 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: d1y1wl_
  • Chain 'N':
    Compound: 5'-d(*ap*ap*gp*tp*ap*cp*t)-3'
    Species: synthetic, synthetic
  • Chain 'P':
    Compound: 5'-r(*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3'
    Species: synthetic, synthetic
  • Chain 'T':
    Compound: 5'-d(p*ap*gp*tp*ap*cp*tp*tp*ap*cp*gp*cp*cp*tp*gp*gp*tp*cp*ap*t)-3'
    Species: synthetic, synthetic
  • Heterogens: ZN, MG

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1y1wA (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)
    >1y1wA (A:)
    vgqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsi
    drnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnel
    mrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglkl
    vgswkdepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvppppvrps
    isfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhvatymdndia
    gqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleldqvgvpks
    iaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskragdiqlqyg
    wkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynadfdgdemnl
    hvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfieldqvlnm
    lywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkdngmliid
    gqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngfstgigdt
    iadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvrflneardka
    grlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdrtlphfsk
    ddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrrlvkaledim
    vhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvdllntdhtld
    psllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqnaqq
    tfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccllrsrlatr
    rvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtlkkvtsgvp
    rlkeilnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydpdpr
    stvipedeeiiqlhfslqqspwllrleldraamndkdltmgqvgerikqtfkndlfviws
    edndekliircrvvaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyv
    kepewvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalykevynviasd
    gsyvnyrhmallvdvmttqggltsvtrhgfnrsntgalmrcsfeetveilfeagasaeld
    dcrgvsenvilgqmapigtgafdvmideeslvkymp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1y1wB (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)
    >1y1wB (B:)
    desapitaedswavisaffrekglvsqqldsfnqfvdytlqdiicedstliisfgkiyvt
    kpmvnesdgvthalypqearlrnltyssglfvdvkkkvfigrlpimlrskncylseates
    dlyklkecpfdmggyfiingsekvliaqersagnivqvfkkaapspishvaeirsalekg
    srfistlqvklygregssartikatlpyikqdipiviifralgiipdgeilehicydvnd
    wqmlemlkpcvedgfviqdretaldfigkekriqyakdilqkeflphitqlegfesrkaf
    flgyminrlllcaldrkdqddrdhfgkkrldlagpllaqlfktlfkkltkdifrymqrtv
    elainaktitsglkyalatgnwgeqkkamssragvsqvlnrytysstlshlrrtntpigr
    dgklakprqlhnthwglvcpaetpegqacglvknlslmscisvgtdpmpiitflsewgme
    pledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkgdinpevsmirdirekel
    kiftdagrvyrplfiveddeslghkelkvrkghiaklmateyqdeytwssllneglveyi
    daeeeesiliamqpedlepaeadvdpakrirvshhattfthceihpsmilgvaasiipfp
    dhnqsprntyqsamgkqamgvfltnynvrmdtmanilyypqkplgttrameylkfrelpa
    gqnaivaiacysgynqedsmimnqssidrglfrslffrsymdqekkygmsitetfekpqr
    tntlrmkhgtydkldddgliapgvrvsgedviigkttpisskrdastplrstengivdqv
    lvttnqdglkfvkvrvrttkipqigdkfasrhgqkgtigityrredmpftaegivpdlii
    nphaipsrmtvahliecllskvaalsgnegdaspftditvegiskllrehgyqsrgfevm
    ynghtgkklmaqiffgptyyqrlrhmvddkiharargpmqvltrqpvegrsrdgglrfge
    merdcmiahgaasflkerlmeasdafrvhicgicglmtviaklnhnqfeckgcdnkidiy
    qihipyaakllfqelmamnitprlytdrsrdf
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1y1wC (C:)
    mseegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvlad
    efiahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlvi
    vsnlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefey
    dpwnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipv
    dqvvvrgidtlqkkvasillaltqmdqdkvnfasgdnntasnmlgsnedvmmtgaeqdpy
    snasqmgntgsggydnaw
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wC (C:)
    eegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvladef
    iahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlvivs
    nlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefeydp
    wnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipvdq
    vvvrgidtlqkkvasillaltqmdqd
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >1y1wD (D:)
    mnvststfqtrrrrlkkveeeenaatlqlgqefqlkqinhqgeeeelialnlsearlvik
    ealverrrafkrsqkkhkkkhlkhenandettavededddldeddvnaddddfmhsetre
    kelesidvlleqttggnnkdlkntmqyltnfsrfrdqetvgaviqllkstglhpfevaql
    gslacdtadeaktlipslnnkisddelerilkelsnletly
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wD (D:)
    ststfqtrrrrlkkveeeenaatlqlgqefqlkqinhqgeeeelialnlsearlvikeal
    verrrafkrsqkktrekelesidvlleqttggnnkdlkntmqyltnfsrfrdqetvgavi
    qllkstglhpfevaqlgslacdtadeaktlipslnnkisddelerilkelsnletly
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >1y1wE (E:)
    mdqenernisrlwrafrtvkemvkdrgyfitqeevelpledfkakycdsmgrpqrkmmsf
    qanpteesiskfpdmgslwvefcdepsvgvktmktfvihiqeknfqtgifvyqnnitpsa
    mklvpsippatietfneaalvvnithhelvpkhirlssdekrellkryrlkesqlpriqr
    adpvalylglkrgevvkiirksetsgryasyricm
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wE (E:)
    dqenernisrlwrafrtvkemvkdrgyfitqeevelpledfkakycdsmgrpqrkmmsfq
    anpteesiskfpdmgslwvefcdepsvgvktmktfvihiqeknfqtgifvyqnnitpsam
    klvpsippatietfneaalvvnithhelvpkhirlssdekrellkryrlkesqlpriqra
    dpvalylglkrgevvkiirksetsgryasyricm
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >1y1wF (F:)
    msdyeeafndgnenfedfdvehfsdeetyeekpqfkdgettdangktivtggngpedfqq
    heqirrktlkekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplri
    amkelaekkiplvirrylpdgsfedwsveelivdl
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wF (F:)
    kaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplriamkelaekkip
    lvirrylpdgsfedwsveelivdl
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1y1wG (G:)
    mffikdlslnitlhpsffgprmkqylktklleevegsctgkfgyilcvldydnidiqrgr
    ilptdgsaefnvkyravvfkpfkgevvdgtvvscsqhgfevqvgpmkvfvtkhlmpqdlt
    fnagsnppsyqssedvitiksrirvkiegcisqvssihaigsikedylgai
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >1y1wH (H:)
    msntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtia
    sslnledtpandssatrswrppqagdrsladdydyvmygtaykfeevskdliavyysfgg
    llmrlegnyrnlnnlkqenayllirr
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wH (H:)
    sntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtias
    sltrswrppqagdrsladdydyvmygtaykfeevskdliavyysfggllmrlegnyrnln
    nlkqenayllirr
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >1y1wI (I:)
    mttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvq
    digsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknkrtq
    fs
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wI (I:)
    ttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvqd
    igsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknkrtq
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >1y1wJ (J:)
    mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
    lrynplekrd
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wJ (J:)
    mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
    lrynp
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >1y1wK (K:)
    mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
    ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtlaaddaf
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wK (K:)
    mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
    ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtl
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >1y1wL (L:)
    msregfqiptnldaaaagtsqartatlkyicaecssklslsrtdavrckdcghrillkar
    tkrlvqfear
    

    Sequence, based on observed residues (ATOM records): (download)
    >1y1wL (L:)
    atlkyicaecssklslsrtdavrckdcghrillkartkrlvqfear
    

  • Chain 'N':
    No sequence available.

  • Chain 'P':
    No sequence available.

  • Chain 'T':
    No sequence available.