PDB entry 2r93

View 2r93 on RCSB PDB site
Description: Elongation complex of RNA polymerase II with a hepatitis delta virus-derived RNA stem loop
Class: Transferase/RNA
Keywords: TRANSFERASE/DNA/RNA, DNA-BINDING, PHOSPHORYLATION, RNA POLYMERASE II, METAL-BINDING, NUCLEAR PROTEIN, TRANSCRIPTION BUBBLE, ELONGATION COMPLEX, TRANSFERASE, TRANSCRIPTION, RNA-DEPENDENT, RNA-DEPENDENT RNA SYNTHESIS, RDRP, DDRP, RNA-BINDING, HEPATITIS DELTA VIRUS, HDV, DNA-directed RNA polymerase, Magnesium, Nucleotidyltransferase, Nucleus, Ubl conjugation, Zinc, Zinc-finger, Polymorphism, Cytoplasm, DNA damage, DNA repair, mRNA processing, Transferase/RNA COMPLEX
Deposited on 2007-09-12, released 2007-11-27
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-02-03.
Experiment type: XRAY
Resolution: 4 Å
R-factor: 0.216
AEROSPACI score: 0.1 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase II subunit RPB1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93a1
  • Chain 'B':
    Compound: DNA-directed RNA polymerase II subunit RPB2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93b1
  • Chain 'C':
    Compound: DNA-directed RNA polymerase II subunit RPB3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: DNA-directed RNA polymerase II subunit RPB4
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93d1
  • Chain 'E':
    Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93f1
  • Chain 'G':
    Compound: DNA-directed RNA polymerase II subunit RPB7
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93g1
  • Chain 'H':
    Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93h1
  • Chain 'I':
    Compound: DNA-directed RNA polymerase II subunit RPB9
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93j1
  • Chain 'K':
    Compound: DNA-directed RNA polymerase II subunit RPB11
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93k1
  • Chain 'L':
    Compound: DNA-directed RNA polymerases I, II, and III subunit RPABC4
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2r93l1
  • Chain 'R':
    Compound: RNA (5'-r(*up*gp*ap*up*up*cp*up*cp*up*ap*up*cp*gp*gp*ap*ap*up*c)-3')
    Species: synthetic, synthetic
  • Heterogens: ZN, MG

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2r93A (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)
    >2r93A (A:)
    vgqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsi
    drnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnel
    mrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglkl
    vgswkkdrdepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvppppv
    rpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhvatymdn
    diagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleldqvgv
    pksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskragdiql
    qygwkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynadfdgde
    mnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfieldqv
    lnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkdngml
    iidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngfstgi
    gdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvrflnear
    dkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdrtlph
    fskddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrrlvkale
    dimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvdllntdh
    tldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqn
    aqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccllrsrl
    atrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtlkkvts
    gvprlkeilnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydp
    dprstvipedeeiiqlhfsllqqspwllrleldraamndkdltmgqvgerikqtfkndlf
    viwsedndekliircrvvrpaeedhmlkkientmlenitlrgveniervvmmkydrkvps
    ptgeyvkepewvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalykevy
    nviasdgsyvnyrhmallvdvmttqggltsvtrhgfnrsntgalmrcsfeetveilfeag
    asaelddcrgvsenvilgqmapigtgafdvmideeslvkymp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2r93B (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)
    >2r93B (B:)
    edesapitaedswavisaffrekglvsqqldsfnqfvdytlqdiicedstliisfgkiyv
    tkpmvnesdgvthalypqearlrnltyssglfvdvkkvfigrlpimlrskncylseates
    dlyklkecpfdmggyfiingsekvliaqersagnivqvfkkaapspishvaeirsalekg
    srfistlqvklygregssartikatlpyikqdipiviifralgiipdgeilehicydvnd
    wqmlemlkpcvedgfviqdretaldfigrrgtalgikkekriqyakdilqkeflphitql
    egfesrkafflgyminrlllcaldrkdqddrdhfgkkrldlagpllaqlfktlfkkltkd
    ifrymqrtvelainaktitsglkyalatgnwgeqkkamssragvsqvlnrytysstlshl
    rrtntpikprqlhnthwglvcpaetpegqacglvknlslmscisvgtdpmpiitflsewg
    mepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkgdinpevsmirdirek
    elkiftdagrvyrplfiveddeslghkelkvrkghiaklmateyqdeytwssllneglve
    yidaeeeesiliamqpedlepaeadvdpakrirvshhattfthceihpsmilgvaasiip
    fpdhnqsprntyqsamgkqamgvfltnynvrmdtmanilyypqkplgttrameylkfrel
    pagqnaivaiacysgynqedsmimnqssidrglfrslffrsymdqekkygmsitetfekp
    qrtntlrmkhgtydkldddgliapgvrvsgedviigkttpskrdastplrstengivdqv
    lvttnqdglkfvkvrvrttkipqigdkfasrhgqkgtigityrredmpftaegivpdlii
    nphaipsrmtvahliecllskvaalsgnegdaspftditvegiskllrehgyqsrgfevm
    ynghtgkklmaqiffgptyyqrlrhmvddkiharargpmqvltrqpvegrsrdgglrfge
    merdcmiahgaasflkerlmeasdafrvhicgicglmtviaklnhnqfeckgcdnkidiy
    qihipyaakllfqelmamnitprlytdrsrdf
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2r93D (D:)
    mnvststfqtrrrrlkkveeeenaatlqlgqefqlkqinhqgeeeelialnlsearlvik
    ealverrrafkrsqkkhkkkhlkhenandettavededddldeddvnaddddfmhsetre
    kelesidvlleqttggnnkdlkntmqyltnfsrfrdqetvgaviqllkstglhpfevaql
    gslacdtadeaktlipslnnkisddelerilkelsnletly
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r93D (D:)
    vststfqtrrrrlkkveeeenaatlqlgqefqlkqinhqgeeeelialnlsearlvikea
    lverrrafkrsqkktrekelesidvlleqttggnnkdlkntmqyltnfsrfrdqetvgav
    iqllkstglhpfevaqlgslacdtadeaktlipslnnkisddelerilkelsnletly
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2r93F (F:)
    msdyeeafndgnenfedfdvehfsdeetyeekpqfkdgettdangktivtggngpedfqq
    heqirrktlkekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplri
    amkelaekkiplvirrylpdgsfedwsveelivdl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r93F (F:)
    tlkekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplriamkelae
    kkiplvirrylpdgsfedwsveelivdl
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2r93G (G:)
    mffikdlslnitlhpsffgprmkqylktklleevegsctgkfgyilcvldydnidiqrgr
    ilptdgsaefnvkyravvfkpfkgevvdgtvvscsqhgfevqvgpmkvfvtkhlmpqdlt
    fnagsnppsyqssedvitiksrirvkiegcisqvssihaigsikedylgai
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >2r93H (H:)
    msntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtia
    sslnledtpandssatrswrppqagdrsladdydyvmygtaykfeevskdliavyysfgg
    llmrlegnyrnlnnlkqenayllirr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r93H (H:)
    sntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtias
    slnltrswrppqagdrsladdydyvmygtaykfeevskdliavyysfggllmrlegnyrn
    lnnlkqenayllirr
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >2r93J (J:)
    mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
    lrynplekrd
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r93J (J:)
    mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
    lrynp
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >2r93K (K:)
    mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
    ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtlaaddaf
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r93K (K:)
    mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
    ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlq
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >2r93L (L:)
    msregfqiptnldaaaagtsqartatlkyicaecssklslsrtdavrckdcghrillkar
    tkrlvqfear
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r93L (L:)
    atlkyicaecssklslsrtdavrckdcghrillkartkrlvqfear
    

  • Chain 'R':
    No sequence available.