PDB entry 2nvy

View 2nvy on RCSB PDB site
Description: RNA Polymerase II form II in 150 mM Mn+2
Class: transcription
Keywords: transcription, mRNA, multiprotein complex, molecular machine, DNA
Deposited on 2006-11-13, released 2006-12-26
The last revision prior to the SCOPe 2.01 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 3.4 Å
R-factor: 0.251
AEROSPACI score: 0.11 (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 2.01: d2nvya1
  • 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 2.01: d2nvyb1
  • 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 2.01: d2nvyc1, d2nvyc2
  • 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 2.01: d2nvye1, d2nvye2
  • 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 2.01: d2nvyf1
  • 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 2.01: d2nvyh1
  • 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 2.01: d2nvyi1, d2nvyi2
  • 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 2.01: d2nvyj1
  • 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 2.01: d2nvyk1
  • 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 2.01: d2nvyl1
  • Heterogens: ZN, MN

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2nvyA (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) 
    >2nvyA (A:)
vgqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsi
drnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnel
mrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglkl
vgswkkdratgdadepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclpv
ppppvrpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhva
tymdndiagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnlel
dqvgvpksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskra
gdiqlqygwkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynad
fdgdemnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfi
eldqvlnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllspk
dngmliidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhng
fstgigdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvrf
lneardkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvd
rtlphfskddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrrl
vkaledimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvdl
lntdhtldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnir
riiqnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccl
lrsrlatrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtl
kkvtsgvprlkeilnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiase
iyydpdprstvipedeeiiqlhfslqqspwllrleldraamndkdltmgqvgerikqtfk
ndlfviwsedndekliircrvvaeedhmlkkientmlenitlrgveniervvmmkydrkv
psptgeyvkepewvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalyke
vynviasdgsyvnyrhmallvdvmttqggltsvtrhgfnrsntgalmrcsfeetveilfe
agasaelddcrgvsenvilgqmapigtgafdvmideesl

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2nvyB (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) 
    >2nvyB (B:)
fedesapitaedswavisaffrekglvsqqldsfnqfvdytlqdiicedstlieisfgki
yvtkpmvnesdgvthalypqearlrnltyssglfvdvkkrtyekvfigrlpimlrskncy
lseatesdlyklkecpfdmggyfiingsekvliaqersagnivqvfkkaapspishvaei
rsalekgsrfistlqvklygregssartikatlpyikqdipiviifralgiipdgeileh
icydvndwqmlemlkpcvedgfviqdretaldfigrrgtalgikkekriqyakdilqkef
lphitqlegfesrkafflgyminrlllcaldrkdqddrdhfgkkrldlagpllaqlfktl
fkkltkdifrymqrtvelainaktitsglkyalatgnwgagvsqvlnrytysstlshlrr
tntpiakprqlhnthwglvcpaetpegqacglvknlslmscisvgtdpmpiitflsewgm
epledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkgdinpevsmirdireke
lkiftdagrvyrplfiveddeslghkelkvrkghiaklmateyqdeytwssllneglvey
idaeeeesiliamqpedlepdvdpakrirvshhattfthceihpsmilgvaasiipfpdh
nqsprntyqsamgkqamgvfltnynvrmdtmanilyypqkplgttrameylkfrelpagq
naivaiacysgynqedsmimnqssidrglfrslffrsymdqekkygmsitetfekpqrtn
tlrmkhgtydkldddgliapgvrvsgedviigkttpisskrdastplrstengivdqvlv
ttnqdglkfvkvrvrttkipqigdkfasrhgqkgtigityrredmpftaegivpdliinp
haipsrmtvahliecllskvaalsgnegdaspftditvegiskllrehgyqsrgfevmyn
ghtgkklmaqiffgptyyqrlrhmvddkiharargpglrfgemerdcmiahgaasflker
lmeasdafrvhicgicglmtviaklnhnqfeckgcdnkidiyqihipyaakllfqelmam
nitprlytdrsrdf

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

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

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2nvyE (E:)
mdqenernisrlwrafrtvkemvkdrgyfitqeevelpledfkakycdsmgrpqrkmmsf
qanpteesiskfpdmgslwvefcdepsvgvktmktfvihiqeknfqtgifvyqnnitpsa
mklvpsippatietfneaalvvnithhelvpkhirlssdekrellkryrlkesqlpriqr
adpvalylglkrgevvkiirksetsgryasyricm

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

    Sequence, based on observed residues (ATOM records): (download) 
    >2nvyF (F:)
kaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplriamkelaekkip
lvirrylpdgsfedwsveelivdl

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

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

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2nvyI (I:)
mttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvq
digsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknkrtq
fs

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

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

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

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

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

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