PDB entry 7k04

View 7k04 on RCSB PDB site
Description: structure of tfiih/rad4-rad23-rad33/dna in dna opening
Deposited on 2020-09-03, released 2021-07-28
The last revision was dated 2021-07-28, with a file datestamp of 2021-07-23.
Experiment type: EM
Resolution: 9.25 Å
R-factor: N/A
AEROSPACI score: -0.06 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: DNA repair helicase rad3
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain '1':
    Compound: General transcription and DNA repair factor IIH subunit TFB1
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P32776 (1-641)
      • insertion (0)
  • Chain '2':
    Compound: General transcription and DNA repair factor IIH subunit TFB2
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain '4':
    Compound: General transcription and DNA repair factor IIH subunit TFB4
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain '5':
    Compound: RNA polymerase II transcription factor B subunit 5
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: TFB5, YDR079C-A
    Database cross-references and differences (RAF-indexed):
  • Chain '6':
    Compound: General transcription and DNA repair factor IIH subunit SSL1
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain '7':
    Compound: DNA repair helicase RAD25
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: SSL2, LOM3, RAD25, UVS112, YIL143C
    Database cross-references and differences (RAF-indexed):
  • Chain 'A':
    Compound: DNA repair protein RAD4
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: RAD4, YER162C
    Database cross-references and differences (RAF-indexed):
    • Uniprot P14736 (0-753)
      • conflict (222)
      • conflict (426)
  • Chain 'E':
    Compound: DNA repair protein RAD33
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: RAD33, YML011C, YM9571.07C
    Database cross-references and differences (RAF-indexed):
  • Chain 'W':
    Compound: Undamaged DNA strand
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'Y':
    Compound: Damaged DNA strand
    Species: synthetic construct, synthetic [TaxId:32630]
  • Heterogens: CA, SF4, 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 '0':
    Sequence, based on SEQRES records:
    >7k040 (0:)
mkfyiddlpvlfpypkiypeqynymcdikktldvggnsilempsgtgktvsllsltiayq
mhypehrkiiycsrtmseiekalvelenlmdyrtkelgyqedfrglgltsrknlclhpev
skerkgtvvdekcrrmtngqakrkleedpeanvelceyhenlynievedylpkgvfsfek
llkyceektlcpyfivrrmislcniiiysyhylldpkiaervsnevskdsivifdeahni
dnvcieslsldlttdalrratrganalderisevrkvdsqklqdeyeklvqglhsadilt
dqeepfvetpvlpqdllteaipgnirraehfvsflkrlieylktrmkvlhvisetpksfl
qhlkqltfierkplrfcserlsllvrtlevtevedftalkdiatfatlistyeegfllii
epyeienaavpnpimrftcldasiaikpvferfssviitsgtispldmyprmlnfktvlq
ksyamtlakksflpmiitkgsdqvaissrfeirndpsivrnygsmlvefakitpdgmvvf
fpsylymesivsmwqtmgildevwkhklilvetpdaqetslaletyrkacsngrgaills
vargkvsegidfdhqygrtvlmigipfqytesrilkarlefmrenyrirendflsfdamr
haaqclgrvlrgkddygvmvladrrfsrkrsqlpkwiaqglsdadlnlstdmaisntkqf
lrtmaqptdpkdqegvsvwsyedlikhqnsrkdqggfienenkegeqdededediemq

    Sequence, based on observed residues (ATOM records):
    >7k040 (0:)
mkfyiddlpvlfpypkiypeqynymcdikktldvggnsilempsgtgktvsllsltiayq
mhypehrkiiycsrtmseiekalvelenlmdyrtkelgyqedfrglgltsrknlclhpev
skerkgtvvdekcrrmtngqakrkleedpeanvelceyhenlynievedylpkgvfsfek
llkyceektlcpyfivrrmislcniiiysyhylldpkiaervsnevskdsivifdeahni
dnvcieslsldlttdalrratrganalderisevrkvdsqklqdeyeklvqglhsadilt
dqeepfvetpvlpqdllteaipgnirraehfvsflkrlieylktrmkvlhvisetpksfl
qhlkqltfierkplrfcserlsllvrtlevtevedftalkdiatfatlistyeegfllii
epyeienaavpnpimrftcldasiaikpvferfssviitsgtispldmyprmlnfktvlq
ksyamtlakksflpmiitkgsdqvaissrfeirndpsivrnygsmlvefakitpdgmvvf
fpsylymesivsmwqtmgildevwkhklilvetpdaqetslaletyrkacsngrgaills
vargkvsegidfdhqygrtvlmigipfqytesrilkarlefmrenyrirendflsfdamr
haaqclgrvlrgkddygvmvladrrfsrkrsqlpkwiaqglsdadlnlstdmaisntkqf
lrtmaqptdpkdqegvsvwsyedlikhqnsrkdq

  • Chain '1':
    Sequence, based on SEQRES records:
    >7k041 (1:)
pshsgaaifekvsgiiainedvspaeltwrstdgdkvhtvvlstidklqatpassekmml
rligkvdeskkrkdnegnevvpkpqrhmfsfnnrtvmdnikmtlqqiisrykdadiyeek
rrreesaqhtetpmssssvtagtptphldtpqlnngaplintaklddslskeklltnlkl
qqsllkgnkvlmkvfqetvinaglppsefwstripllrafalstsqkvgpynvlstikpv
assenkvnvnlsrekilnifenypivkkaytdnvpknfkepefwarffssklfrklrgek
imqndrgdviidryltldqefdrkdddmllhpvkkiidldgniqddpvvrgnrpdftmqp
gvdingnsdgtvdilkgmnrlsekmimalkneysrtnlqnksnitndeededndernelk
iddlnesyktnyaiihlkrnahekttdndakssadsiknadlkvsnqqmlqqlslvmdnl
inkldlnqvvpnnevsnkinkrvitaikinakqakhnnvnsalgsfvdntsqanelevks
tlpidllescrmlhttcceflkhfyihfqsgeqkqastvkklynhlkdcieklnelfqdv
lngdgesmsntctaylkpvlnsitlathkydeyfneynnnsn

    Sequence, based on observed residues (ATOM records):
    >7k041 (1:)
pshsgaaifekvsgiiainedvspaeltwrstdgdkvhtvvlstidklqatpassekmml
rligkvdeskkrkdnegnevvpkpqrhmfsfnnrtvmdnikmtlqqiisrykdadiyeek
slskeklltnlklqqsllkgnkvlmkvfqetvinaglppsefwstripllrafalstsqk
vgpynvlstikpvassenkvnvnlsrekilnifenypivkkaytdnvpknfkepefwarf
fssklfrklrgekimqndrgdviidryltldqefdrkdddmllhpvkkiidldgniqddp
vvrgnrpdsdgtvdilkgmnrlsekmimalkneysnqqmlqqlslvmdnlinkldlnqvv
pnnevsnkinkrvitaikinakqakhnnvevkstlpidllescrmlhttcceflkhfyih
qkqastvkklynhlkdcieklnelfqdvlngdgesmsntctaylkpvlnsitlathkyde
yfneynn

  • Chain '2':
    Sequence, based on SEQRES records:
    >7k042 (2:)
msdyslkhsvtqyleeipqqvqnrlytspatclaiyrilpplakffimamvfnenevpll
dldkwvnsngklqfqnaiksmkslhllipnkssgtlminlnptfkislrnaltggevqns
fgvvveenvvsldlldeysankwetilhfmvgtplakipsekvlnllkhsklmeevnstg
efkitnegfqfllqeinsqlwtlllqylkmietskmdlvdvlhfifmlgalevgkaykid
alsetqrimlqdmrdyglvfqkhsndsifyptklalmltsdtktirsasnamdsvlrqnr
eepsvnedgangksttdittsddlnkaglknqdipdgslivetnfkiysysnsplqiavl
slfvhlkarfvnmvlgqitresirraltngitadqiiaylethahpqmrrlaeeklekkl
eldpnckeplqvlpptvvdqirlwqleldrvityegslysdfetsqeynllskyaqdigv
llwkddkkkkffiskegnsqvldfakrklkkkq

    Sequence, based on observed residues (ATOM records):
    >7k042 (2:)
khsvtqyleeipqqvqnrlytspatclaiyrilpplakffimamvfnenevplldldkwv
nsngklqfqnaiksmkslhllipnkssgtlminlnptfkislrnaltggevqnsfgvvve
envvsldlldeysankwetilhfmvgtplakipsekvlnllkhsklmeevnstgefkitn
egfqfllqeinsqlwtlllqylkmietskmdlvdvlhfifmlgalevgkaykidalsetq
rimlqdmrdyglvfqkhsndsifyptklalmltsdtktirglknqdipdgslivetnfki
ysysnsplqiavlslfvhlkarfvnmvlgqitresirraltngitadqiiaylethahpq
mrrlaeeklekkleldpnckeplqvlpptvvdqirlwqleldrvityegslysdfetsqe
ynllskyaqdigvllwkddkkkkffiskegnsqvldfakr

  • Chain '4':
    Sequence, based on SEQRES records:
    >7k044 (4:)
mdaisdptfkharsrkqvteespslltviieiapklwttfdeegnekgsiikvlealivf
lnahlafnsankvaviaaysqgikylypestsalkasesenktrsdlkiinsdmyrrfrn
vdetlveeiyklfelekkqieqnsqrstlagamsagltyvnriskesvttslksrllvlt
cgsgsskdeifqyipimncifsatkmkcpidvvkiggskestflqqttdatngvylhves
tegliqylatamfidpslrpiivkpnhgsvdfrtscyltgrvvavgficsvclcvlsiip
pgnkcpacdsqfdehviaklkrkpvvprlkakkkvtkp

    Sequence, based on observed residues (ATOM records):
    >7k044 (4:)
spslltviieiapklwttfdeegnekgsiikvlealivflnahlafnsankvaviaaysq
gikylypestsaldmyrrfrnvdetlveeiyklfelekkqieqnsqrstlagamsaglty
vnriskesvttslksrllvltcgsgsskdeifqyipimncifsatkmkcpidvvkiggsk
estflqqttdatngvylhvestegliqylatamfidpslrpiivkpnhgsvdfrtscylt
grvvavgficsvclcvlsiippgnkcpacdsqfdehviaklkrk

  • Chain '5':
    Sequence, based on SEQRES records:
    >7k045 (5:)
mararkgalvqcdpsikalilqidakmsdivleelddthllvnpskvefvkhelnrllsk
niynpmdeeenq

    Sequence, based on observed residues (ATOM records):
    >7k045 (5:)
ararkgalvqcdpsikalilqidakmsdivleelddthllvnpskvefvkhelnrllskn
iynpmd

  • Chain '6':
    Sequence, based on SEQRES records:
    >7k046 (6:)
mapvviseseededrvaitrrtkrqvhfdgegddrvdqqqqqhssshrdrdkhvqrkkkk
rlsnrnlqgsnggyawedeikrswdlvkvddegdmaslvasivearkkrtakknitpyqr
giirsliltldcseamlekdlrpnrhamiiqyaidfvheffdqnpisqmgiiimrnglaq
lvsqvsgnpqdhidalksirkqepkgnpslqnalemarglllpvpahctrevlivfgsls
ttdpgdihqtidslvsekirvkvlglsaqvaickelckatnygdesfykilldethlkel
fneavtplpvnkinkgftlvkmgfptrifedtptfcschsklvyggyfcpnchskvcslp
tvcpccdlmlilsthlarsyhhlmplktfaevpttekfrsedcfscqsrfpilknhkngk
lltssryrcedckqefcvdcdvfiheilhncpgceskpvit

    Sequence, based on observed residues (ATOM records):
    >7k046 (6:)
kkrtakknitpyqrgiirsliltldcseamlekdlrpnrhamiiqyaidfvheffdqnpi
sqmgiiimrnglaqlvsqvsgnpqdhidalksirkqepkgnpslqnalemarglllpvpa
hctrevlivfgslsttdpgdihqtidslvsekirvkvlglsaqvaickelckatnygdes
fykilldethlkelfneavtplpvnkinkgftlvkmgfptrifedtptfcschsklvygg
yfcpnchskvcslptvcpccdlmlilsthlarsyhhlmplktfaevpttekfrsedcfsc
qsrfpilknhkngklltssryrcedckqefcvdcdvfiheilhncpgcesk

  • Chain '7':
    Sequence, based on SEQRES records:
    >7k047 (7:)
mtdvegyqpkskgkifpdmgesffssdedspatdaeidenyddnretsegrgerdtgamv
tglkkprkktkssrhtaadssmnqmdakdkallqdtnsdipadfvpdsvsgmfrshdfsy
lrlrpdhasrplwispsdgriilesfsplaeqaqdflvtiaepisrpshiheykitaysl
yaavsvgletddiisvldrlskvpvaesiinfikgatisygkvklvikhnryfvettqad
ilqmllndsvigplridsdhqvqppedvlqqqlqqtagkpatnvnpndveavfsaviggd
nereeedddidavhsfeianesvevvkkrcqeidypvleeydfrndhrnpdldidlkpst
qirpyqekslskmfgngrarsgiivlpcgagktlvgitaactikksvivlctssvsvmqw
rqqflqwctlqpencavftsdnkemfqtesglvvstysmvantrnrshdsqkvmdfltgr
ewgfiildevhvvpaamfrrvvstiaahaklgltatlvreddkigdlnfligpklyeanw
melsqkghianvqcaevwcpmtaefyqeylretarkrmllyimnptkfqacqfliqyher
rgdkiivfsdnvyalqeyalkmgkpfiygstpqqermnilqnfqyndqintiflskvgdt
sidlpeatcliqisshygsrrqeaqrlgrilrakrrndegfnaffyslvskdtqemyyst
krqaflvdqgyafkvithlhgmenipnlayasprerrellqevllkneeaagievgddad
nsvgrgsnghkrfkskavrgegslsglaggedmaymeystnknkelkehhplirkmyykn
lkk

    Sequence, based on observed residues (ATOM records):
    >7k047 (7:)
padfvpdsvsgmfrshdfsylrlrpdhasrplwispsdgriilesfsplaeqaqdflvti
aepisrpshiheykitayslyaavsvgletddiisvldrlskvpvaesiinfikgatisy
gkvklvikhnryfvettqadilqmllndsvigplridsdhqvqppedvlereeedddida
vhsfeianesvevvkkrcqeidypvleeydfrndhrnpdldidlkpstqirpyqekslsk
mfgngrarsgiivlpcgagktlvgitaactikksvivlctssvsvmqwrqqflqwctlqp
encavftsdnkemfqtesglvvstysmvantrnrshdsqkvmdfltgrewgfiildevhv
vpaamfrrvvstiaahaklgltatlvreddkigdlnfligpklyeanwmelsqkghianv
qcaevwcpmtaefyqeylretarkrmllyimnptkfqacqfliqyherrgdkiivfsdnv
yalqeyalkmgkpfiygstpqqermnilqnfqyndqintiflskvgdtsidlpeatcliq
isshygsrrqeaqrlgrilrakrrndegfnaffyslvskdtqemyystkrqaflvdqgya
fkvithlhgmenipnlayasprerrellqevllkneea

  • Chain 'A':
    Sequence, based on SEQRES records:
    >7k04A (A:)
mnedlpkeyfelirkalnekeaekaplsrrrrvrrknqplpdakkkfktglnelpresvv
tvnldssddgvvtvptddsveeiqsseedydseefedvtdgnevagvedisveikpsskr
nsdarrtsrnvcsneerkrrkyfhmlylvclmvhgfirnewinskrlsrklsnlvpekvf
ellhpqkdeelplrstrklldglkkcmelwqkhwkitkkydneglymrtwkeiemsannk
rkfktlkrsdflravskghgdpdisvqgfvamlracnvnarlimscqppdftnmkidtsl
ngnnaykdmvkypifwcevwdkfskkwitvdpvnlktieqvrlhsklapkgvaccernml
ryviaydrkygcrdvtrryaqwmnskvrkrritkddfgekwfrkvitalhhrkrtkiddy
edqyffrrdesegipdsvqdlknhpyyvleqdikqtqivkpgckecgylkvhgkvgkvlk
vyakrdiadlksarqwymngrilktgsrckkvikrtvgrpkgeaeeederlysfedtely
ipplasasgeitkntfgnievfaptmipgncclvenpvaikaarflgvefapavtsfkfe
rgstvkpvlsgivvakwlreaietaidgiefiqeddnrkehllgaleswntlllklrirs
klnstygkiaeeepnvtkeqniadnhdntetfmgggflpgianhearpysepsepedsld
yvsvdkaeesatdddvgedysdfmkelemseesd

    Sequence, based on observed residues (ATOM records):
    >7k04A (A:)
ydseefedvtdgnevrnvcsneerkrrkyfhmlylvclmvhgfirnewinskrlsrklsn
lvpekvfellhpqkdeelplrstrklldglkkcmelwqkhwkitkkydneglymrtwkei
emsannkrkfktlkrsdflravskghgdpdisvqgfvamlracnvnarlimscqppdftn
mkidtslngnnaykdmvkypifwcevwdkfskkwitvdpvnlktieqvrlhsklapkgva
ccernmlryviaydrkygcrdvtrryaqwmnskvrkrritkddfgekwfrkvitalhhrk
rtkiddyedqyffrrdesegipdsvqdlknhpyyvleqdikqtqivkpgckecgylkvhg
kvgkvlkvyakrdiadlksarqwymngrilktgsrckkvikrtveederlysfedtelyi
pplasasgeitkntfgnievfaptmipgncclvenpvaikaarflgvefapavtsfkfer
gstvkpvlsgivvakwlreaietaidgswntlllklrirsklns

  • Chain 'E':
    Sequence, based on SEQRES records:
    >7k04E (E:)
mskstnvsyervelfenpkvpievedeilekyaessldhdmtvnelprffkdlqleptiw
klvrnedviiegtdvidftklvrctcqllilmnnltviddlwsmlirncgrdvdfpqval
rdhvlsvkdlqkisnligadqssgtiemiscatdgkrlfmtyldfgcvlgklgylkm

    Sequence, based on observed residues (ATOM records):
    >7k04E (E:)
nltviddlwsmlirncvlsvkdlqkisnligadqssgtiemiscatdgkrlfmtyldfgc
vl

  • Chain 'W':
    No sequence available.

  • Chain 'Y':
    No sequence available.