PDB entry 3gtk

View 3gtk on RCSB PDB site
Description: backtracked rna polymerase ii complex with 18mer rna
Deposited on 2009-03-27, released 2009-06-09
The last revision was dated 2017-11-01, with a file datestamp of 2017-10-27.
Experiment type: XRAY
Resolution: 3.8 Å
R-factor: N/A
AEROSPACI score: 0.04 (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):
  • Chain 'B':
    Compound: DNA-directed RNA polymerase II subunit RPB2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: DNA-directed RNA polymerase II subunit RPB3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • 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):
  • 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):
  • 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):
  • Chain 'K':
    Compound: DNA-directed RNA polymerase II subunit RPB11
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • 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):
  • Chain 'N':
    Compound: DNA (5'-d(*cp*tp*gp*cp*tp*tp*ap*tp*cp*gp*gp*tp*ap*g)-3')
    Species: synthetic, synthetic
  • Chain 'R':
    Compound: DNA/RNA (5'-r(*ap*up*cp*gp*ap*gp*ap*gp*gp*ap*up*gp*c)-d(p*ap*gp*ap*cp*g)-3')
    Species: synthetic, synthetic
  • Chain 'T':
    Compound: DNA (29-mer)
    Species: synthetic, synthetic
  • Heterogens: ZN

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >3gtkA (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):
    >3gtkA (A:)
gqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsid
rnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnelm
rqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglklv
gswkkdratgdadepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvp
pppvrpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhvat
ymdndiagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleld
qvgvpksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskrag
diqlqygwkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynadf
dgdemnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfie
ldqvlnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkd
ngmliidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngf
stgigdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvrfl
neardkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdr
tlphfskddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrrlv
kaledimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvdll
ntdhtldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirr
iiqnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccll
rsrlatrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtln
tfhfagvaskkvtsgvprlkeilnvaknmktpsltvylepghaadqeqaklirsaiehtt
lksvtiaseiyydpdprstvipedeeiiqlhfslldeqqspwllrleldraamndkdltm
gqvgerikqtfkndlfviwsedndekliircrvvrpksldaeteaeedhmlkkientmle
nitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvpgidptriyt
nsfidimevlgieagraalykevynviasdgsyvnyrhmallvdvmttqggltsvtrhgf
nrsntgalmrcsfeetveilfeagasaelddcrgvsenvilgqmapigtgafdvmidees
lv

  • Chain 'B':
    Sequence, based on SEQRES records:
    >3gtkB (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):
    >3gtkB (B:)
desapitaedswavisaffrekglvsqqldsfnqfvdytlqdiicedstlileqlaqhtt
esdnisrkyeisfgkiyvtkpmvnesdgvthalypqearlrnltyssglfvdvkkkvfig
rlpimlrskncylseatesdlyklkecpfdmggyfiingsekvliaqersagnivqvfkk
aapspishvaeirsalekgsrfistlqvklygregssartikatlpyikqdipiviifra
lgiipdgeilehicydvndwqmlemlkpcvedgfviqdretaldfigrrgtalgikkekr
iqyakdilqkeflphitqlegfesrkafflgyminrlllcaldrkdqddrdhfgkkrldl
agpllaqlfktlfkkltkdifrymqrtveeahdfnmklainaktitsglkyalatgnwge
qkkamssragvsqvlnrytysstlshlrrtntpiakprqlhnthwglvcpaetpegqacg
lvknlslmscisvgtdpmpiitflsewgmepledyvphqspdatrvfvngvwhgvhrnpa
rlmetlrtlrrkgdinpevsmirdirekelkiftdagrvyrplfiveddeslghkelkvr
kghiaklmateyqdieggfedveeytwssllneglveyidaeeeesiliamqpedlepae
aneendldvdpakrirvshhattfthceihpsmilgvaasiipfpdhnqsprntyqsamg
kqamgvfltnynvrmdtmanilyypqkplgttrameylkfrelpagqnaivaiacysgyn
qedsmimnqssidrglfrslffrsymdqekkygmsitetfekpqrtntlrmkhgtydkld
ddgliapgvrvsgedviigkttpisskrdastplrstengivdqvlvttnqdglkfvkvr
vrttkipqigdkfasrhgqkgtigityrredmpftaegivpdliinphaipsrmtvahli
ecllskvaalsgnegdaspftditvegiskllrehgyqsrgfevmynghtgkklmaqiff
gptyyqrlrhmvddkiharargpmqvltrqpvegrsrdgglrfgemerdcmiahgaasfl
kerlmeasdafrvhicgicglmtviaklnhnqfeckgcdnkidiyqihipyaakllfqel
mamnitprlytdr

  • Chain 'C':
    Sequence, based on SEQRES records:
    >3gtkC (C:)
mseegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvlad
efiahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlvi
vsnlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefey
dpwnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipv
dqvvvrgidtlqkkvasillaltqmdqdkvnfasgdnntasnmlgsnedvmmtgaeqdpy
snasqmgntgsggydnaw

    Sequence, based on observed residues (ATOM records):
    >3gtkC (C:)
seegpqvkireaskdnvdfilsnvdlamanslrrvmiaeiptlaidsvevetnttvlade
fiahrlgliplqsmdieqleysrdcfcedhcdkcsvvltlqafgesesttnvyskdlviv
snlmgrnighpiiqdkegngvlicklrkgqelkltcvakkgiakehakwgpaaaiefeyd
pwnklkhtdywyeqdsakewpqsknceyedppnegdpfdykaqadtfymnvesvgsipvd
qvvvrgidtlqkkvasillaltqmdqdkvnf

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >3gtkE (E:)
mdqenernisrlwrafrtvkemvkdrgyfitqeevelpledfkakycdsmgrpqrkmmsf
qanpteesiskfpdmgslwvefcdepsvgvktmktfvihiqeknfqtgifvyqnnitpsa
mklvpsippatietfneaalvvnithhelvpkhirlssdekrellkryrlkesqlpriqr
adpvalylglkrgevvkiirksetsgryasyricm

  • Chain 'F':
    Sequence, based on SEQRES records:
    >3gtkF (F:)
msdyeeafndgnenfedfdvehfsdeetyeekpqfkdgettdangktivtggngpedfqq
heqirrktlkekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplri
amkelaekkiplvirrylpdgsfedwsveelivdl

    Sequence, based on observed residues (ATOM records):
    >3gtkF (F:)
ekaipkdqrattpymtkyerarilgtralqismnapvfvdlegetdplriamkelaekki
plvirrylpdgsfedwsveelivdl

  • Chain 'H':
    Sequence, based on SEQRES records:
    >3gtkH (H:)
msntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtia
sslnledtpandssatrswrppqagdrsladdydyvmygtaykfeevskdliavyysfgg
llmrlegnyrnlnnlkqenayllirr

    Sequence, based on observed residues (ATOM records):
    >3gtkH (H:)
msntlfddifqvsevdpgrynkvcrieaasttqdqckltldinvelfpvaaqdsltvtia
sslsatrswrppqagdrsladdydyvmygtaykfeevskdliavyysfggllmrlegnyr
nlnnlkqenayllirr

  • Chain 'I':
    Sequence, based on SEQRES records:
    >3gtkI (I:)
mttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvq
digsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknkrtq
fs

    Sequence, based on observed residues (ATOM records):
    >3gtkI (I:)
ttfrfcrdcnnmlypredkennrllfecrtcsyveeagsplvyrhelitnigetagvvqd
igsdptlprsdrecpkchsrenvffqsqqrrkdtsmvlffvclscshiftsdqknkrtq

  • Chain 'J':
    Sequence, based on SEQRES records:
    >3gtkJ (J:)
mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
lrynplekrd

    Sequence, based on observed residues (ATOM records):
    >3gtkJ (J:)
mivpvrcfscgkvvgdkwesylnllqedeldegtalsrlglkryccrrmilthvdliekf
lrynp

  • Chain 'K':
    Sequence, based on SEQRES records:
    >3gtkK (K:)
mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtlaaddaf

    Sequence, based on observed residues (ATOM records):
    >3gtkK (K:)
mnapdrfelfllgegesklkidpdtkapnavvitfekedhtlgnliraellndrkvlfaa
ykvehpffarfklriqttegydpkdalknacnsiinklgalktnfetewnlqtl

  • Chain 'L':
    Sequence, based on SEQRES records:
    >3gtkL (L:)
msregfqiptnldaaaagtsqartatlkyicaecssklslsrtdavrckdcghrillkar
tkrlvqfear

    Sequence, based on observed residues (ATOM records):
    >3gtkL (L:)
atlkyicaecssklslsrtdavrckdcghrillkartkrlvqfear

  • Chain 'N':
    No sequence available.

  • Chain 'R':
    No sequence available.

  • Chain 'T':
    No sequence available.