PDB entry 2ja6

View 2ja6 on RCSB PDB site
Description: cpd lesion containing RNA polymerase II elongation complex b
Class: transferase
Keywords: DNA-directed RNA polymerase, lesion recognition, transferase/DNA/RNA, DNA damage, zinc-finger, DNA-binding, photolesion, phosphorylation, misincorporation, RNA polymerase II, transcription- coupled repair, tcr, cpd, zinc, arrest, stalling, DNA lesion, metal-binding, nuclear protein, transcription bubble, nucleotidyltransferase, damage recognition, elongation complex, transferase, thymine dimer, transcription, cyclobutane pyrimidine dimer
Deposited on 2006-11-23, released 2007-02-20
The last revision prior to the SCOPe 2.05 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 4 Å
R-factor: 0.2923
AEROSPACI score: 0.02 (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 2.05: d2ja6a1
  • 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 2.05: d2ja6b1
  • Chain 'C':
    Compound: DNA-directed RNA polymerase II 45kda polypeptide
    Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d2ja6c1, d2ja6c2
  • Chain 'D':
    Compound: DNA-directed RNA polymerase II 32kda polypeptide
    Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d2ja6d1
  • 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 2.05: d2ja6e1, d2ja6e2
  • 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 2.05: d2ja6f1
  • Chain 'G':
    Compound: DNA-directed RNA polymerase II 19kda polypeptide
    Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d2ja6g1, d2ja6g2
  • 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 2.05: d2ja6h1
  • 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 2.05: d2ja6i1, d2ja6i2
  • 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 2.05: d2ja6j1
  • 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 2.05: d2ja6k1
  • 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 2.05: d2ja6l1
  • Chain 'N':
    Compound: 5'-d(*tp*ap*ap*gp*tp*ap*cp*tp*tp*gp *ap*gp*cp*t)-3'
    Species: synthetic, synthetic
  • Chain 'P':
    Compound: 5'-r(*up*up*cp*gp*ap*cp*cp*ap*gp*gp*ap)-3'
    Species: synthetic, synthetic
  • Chain 'T':
    Compound: 5'-d(*ap*gp*cp*tp*cp*ap*ap*gp*tp*ap *cp*tp*tp*ttp*tp*cp*cp*brup*gp*gp*tp*cp*ap*tp*t)-3'
    Species: synthetic, synthetic
  • Heterogens: MG, ZN

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2ja6A (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)
    >2ja6A (A:)
    vgqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsi
    drnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnel
    mrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglkl
    vgswkkdrdepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvppppv
    rpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhvatymdn
    diagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleldqvgv
    pksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskragdiql
    qygwkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynadfdgde
    mnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfieldqv
    lnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkdngml
    iidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngfstgi
    gdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvrflnear
    dkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdrtlph
    fskddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrrlvkale
    dimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvdllntdh
    tldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqn
    aqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccllrsrl
    atrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtlkkvts
    gvprlkeilnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydp
    dprstvipedeeiiqlhfslqqspwllrleldraamndkdltmgqvgerikqtfkndlfv
    iwsedndekliircrvvrpaeedhmlkkientmlenitlrgveniervvmmkydrkvpsp
    tgeyvkepewvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalykevyn
    viasdgsyvnyrhmallvdvmttqggltsvtrhgfnrsntgalmrcsfeetveilfeaga
    saelddcrgvsenvilgqmapigtgafdvmideeslvkymp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2ja6B (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)
    >2ja6B (B:)
    fedesapitaedswavisaffrekglvsqqldsfnqfvdytlqdiicedstliisfgkiy
    vtkpmvnesdgvthalypqearlrnltyssglfvdvkkvfigrlpimlrskncylseate
    sdlyklkecpfdmggyfiingsekvliaqersagnivqvfkkaapspishvaeirsalek
    gsrfistlqvklygregssartikatlpyikqdipiviifralgiipdgeilehicydvn
    dwqmlemlkpcvedgfviqdretaldfigrrgtalgikkekriqyakdilqkeflphitq
    legfesrkafflgyminrlllcaldrkdqddrdhfgkkrldlagpllaqlfktlfkkltk
    difrymqrtvelainaktitsglkyalatgnwgeqkkamssragvsqvlnrytysstlsh
    lrrtntpikprqlhnthwglvcpaetpegqacglvknlslmscisvgtdpmpiitflsew
    gmepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkgdinpevsmirdire
    kelkiftdagrvyrplfiveddeslghkelkvrkghiaklmateyqdeytwssllneglv
    eyidaeeeesiliamqpedlepaeadvdpakrirvshhattfthceihpsmilgvaasii
    pfpdhnqsprntyqsamgkqamgvfltnynvrmdtmanilyypqkplgttrameylkfre
    lpagqnaivaiacysgynqedsmimnqssidrglfrslffrsymdqekkygmsitetfek
    pqrtntlrmkhgtydkldddgliapgvrvsgedviigkttpisskrdastplrstengiv
    dqvlvttnqdglkfvkvrvrttkipqigdkfasrhgqkgtigityrredmpftaegivpd
    liinphaipsrmtvahliecllskvaalsgnegdaspftditvegiskllrehgyqsrgf
    evmynghtgkklmaqiffgptyyqrlrhmvddkiharargpmqvltrqpvegrsrdgglr
    fgemerdcmiahgaasflkerlmeasdafrvhicgicglmtviaklnhnqfeckgcdnki
    diyqihipyaakllfqelmamnitprlytdrsrdf
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2ja6C (C:)
    mseegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvlad
    efiahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlvi
    vsnlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefey
    dpwnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipv
    dqvvvrgidtlqkkvasillaltqmdqdkvnfasgdnntasnmlgsnedvmmtgaeqdpy
    snasqmgntgsggydnaw
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6C (C:)
    seegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvlade
    fiahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlviv
    snlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefeyd
    pwnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipvd
    qvvvrgidtlqkkvasillaltqmdqd
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2ja6D (D:)
    mnvststfqtrrrrlkkveeeenaatlqlgqefqlkqinhqgeeeelialnlsearlvik
    ealverrrafkrsqkkhkkkhlkhenandettavededddldeddvnaddddfmhsetre
    kelesidvlleqttggnnkdlkntmqyltnfsrfrdqetvgaviqllkstglhpfevaql
    gslacdtadeaktlipslnnkisddelerilkelsnletly
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6D (D:)
    ststfqtrrrrlkkveeeenaatlqlgqefqlkqinhqgeeeelialnlsearlvikeal
    verrrafkrsqkktrekelesidvlleqttggnnkdlkntmqyltnfsrfrdqetvgavi
    qllkstglhpfevaqlgslacdtadeaktlipslnnkisddelerilkelsnletly
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2ja6E (E:)
    mdqenernisrlwrafrtvkemvkdrgyfitqeevelpledfkakycdsmgrpqrkmmsf
    qanpteesiskfpdmgslwvefcdepsvgvktmktfvihiqeknfqtgifvyqnnitpsa
    mklvpsippatietfneaalvvnithhelvpkhirlssdekrellkryrlkesqlpriqr
    adpvalylglkrgevvkiirksetsgryasyricm
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6E (E:)
    dqenernisrlwrafrtvkemvkdrgyfitqeevelpledfkakycdsmgrpqrkmmsfq
    anpteesiskfpdmgslwvefcdepsvgvktmktfvihiqeknfqtgifvyqnnitpsam
    klvpsippatietfneaalvvnithhelvpkhirlssdekrellkryrlkesqlpriqra
    dpvalylglkrgevvkiirksetsgryasyricm
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2ja6F (F:)
    msdyeeafndgnenfedfdvehfsdeetyeekpqfkdgettdangktivtggngpedfqq
    heqirrktlkekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplri
    amkelaekkiplvirrylpdgsfedwsveelivdl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6F (F:)
    lkekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplriamkelaek
    kiplvirrylpdgsfedwsveelivdl
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2ja6G (G:)
    mffikdlslnitlhpsffgprmkqylktklleevegsctgkfgyilcvldydnidiqrgr
    ilptdgsaefnvkyravvfkpfkgevvdgtvvscsqhgfevqvgpmkvfvtkhlmpqdlt
    fnagsnppsyqssedvitiksrirvkiegcisqvssihaigsikedylgai
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >2ja6H (H:)
    msntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtia
    sslnledtpandssatrswrppqagdrsladdydyvmygtaykfeevskdliavyysfgg
    llmrlegnyrnlnnlkqenayllirr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6H (H:)
    sntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtias
    slnltrswrppqagdrsladdydyvmygtaykfeevskdliavyysfggllmrlegnyrn
    lnnlkqenayllirr
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >2ja6I (I:)
    mttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvq
    digsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknkrtq
    fs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6I (I:)
    ttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvqd
    igsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknk
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >2ja6J (J:)
    mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
    lrynplekrd
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6J (J:)
    mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
    lrynp
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >2ja6K (K:)
    mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
    ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtlaaddaf
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6K (K:)
    mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
    ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtl
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >2ja6L (L:)
    msregfqiptnldaaaagtsqartatlkyicaecssklslsrtdavrckdcghrillkar
    tkrlvqfear
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ja6L (L:)
    atlkyicaecssklslsrtdavrckdcghrillkartkrlvqfear
    

  • Chain 'N':
    No sequence available.

  • Chain 'P':
    No sequence available.

  • Chain 'T':
    No sequence available.