PDBe 5oqj

Electron Microscopy
4.7Å resolution

STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 31-mer (preferred)
Entry contents:
29 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (31 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
DNA-directed RNA polymerase II subunit RPB2 Chain: B
DNA-directed RNA polymerase II subunit RPB3 Chain: C
Molecule details ›
Chain: C
Length: 318 amino acids
Theoretical weight: 35.33 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P16370 (Residues: 1-318; Coverage: 100%)
Gene names: RPB3, YIL021W
Sequence domains:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20433 (Residues: 1-221; Coverage: 100%)
Gene names: J0654, RPB4, YJL140W
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P34087 (Residues: 1-171; Coverage: 100%)
Gene names: D9509.22, RPB7, YDR404C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P27999 (Residues: 1-122; Coverage: 100%)
Gene names: RPB9, YGL070C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Gene names: RPB10, YOR210W
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase II subunit RPB11 Chain: K
Molecule details ›
Chain: K
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Gene names: RPB11, YOL005C
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription initiation factor IIB Chain: M
Molecule details ›
Chain: M
Length: 345 amino acids
Theoretical weight: 38.26 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P29055 (Residues: 1-345; Coverage: 100%)
Gene names: P9513.4, SUA7, YPR086W
Sequence domains:
TATA-box-binding protein Chain: O
Molecule details ›
Chain: O
Length: 240 amino acids
Theoretical weight: 27.04 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13393 (Residues: 1-240; Coverage: 100%)
Gene names: BTF1, SPT15, TBP1, YER148W
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
Transcription initiation factor IIF subunit alpha Chain: Q
Molecule details ›
Chain: Q
Length: 735 amino acids
Theoretical weight: 82.32 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P41895 (Residues: 1-735; Coverage: 100%)
Gene names: G7526, SSU71, TFG1, YGR186W
Sequence domains: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
Transcription initiation factor IIF subunit beta Chain: R
Molecule details ›
Chain: R
Length: 400 amino acids
Theoretical weight: 46.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P41896 (Residues: 1-400; Coverage: 100%)
Gene names: TFG2, YGR005C
Sequence domains:
Transcription initiation factor IIA large subunit Chain: U
Molecule details ›
Chain: U
Length: 286 amino acids
Theoretical weight: 32.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32773 (Residues: 1-286; Coverage: 100%)
Gene names: TOA1, YOR194C
Sequence domains: Transcription factor IIA, alpha/beta subunit
Transcription initiation factor IIA subunit 2 Chain: V
Molecule details ›
Chain: V
Length: 122 amino acids
Theoretical weight: 13.47 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32774 (Residues: 1-122; Coverage: 100%)
Gene names: TOA2, YKL058W
Sequence domains:
Transcription initiation factor IIE subunit alpha Chain: W
Molecule details ›
Chain: W
Length: 586 amino acids
Theoretical weight: 57.54 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36100 (Residues: 1-409, 410-482; Coverage: 100%)
Gene names: TFA1, YKL028W
Sequence domains:
Transcription initiation factor IIE subunit beta Chain: X
Molecule details ›
Chain: X
Length: 328 amino acids
Theoretical weight: 37.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36145 (Residues: 1-328; Coverage: 100%)
Gene names: TFA2, YKR062W
Sequence domains:
General transcription and DNA repair factor IIH helicase subunit XPD Chain: 0
Molecule details ›
Chain: 0
Length: 778 amino acids
Theoretical weight: 89.06 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P06839 (Residues: 1-778; Coverage: 100%)
Gene names: RAD3, REM1, YER171W
Sequence domains:
General transcription and DNA repair factor IIH subunit TFB1 Chain: 1
Molecule details ›
Chain: 1
Length: 641 amino acids
Theoretical weight: 65.44 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32776 (Residues: 1-642; Coverage: 100%)
Gene names: D9740.3, TFB1, YDR311W
Sequence domains:
General transcription and DNA repair factor IIH subunit TFB2 Chain: 2
Molecule details ›
Chain: 2
Length: 462 amino acids
Theoretical weight: 48.41 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q02939 (Residues: 1-513; Coverage: 90%)
Gene names: TFB2, YPL122C
Sequence domains:
RNA polymerase II transcription factor B subunit 3 Chain: 3
Molecule details ›
Chain: 3
Length: 321 amino acids
Theoretical weight: 38.19 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q03290 (Residues: 1-321; Coverage: 100%)
Gene names: RIG2, TFB3, YDR460W
Sequence domains:
General transcription and DNA repair factor IIH subunit TFB4 Chain: 4
Molecule details ›
Chain: 4
Length: 338 amino acids
Theoretical weight: 36.4 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q12004 (Residues: 1-338; Coverage: 100%)
Gene names: TFB4, YPR056W
Sequence domains: Transcription factor Tfb4
General transcription and DNA repair factor IIH subunit TFB5 Chain: 5
Molecule details ›
Chain: 5
Length: 72 amino acids
Theoretical weight: 8.24 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q3E7C1 (Residues: 1-72; Coverage: 100%)
Gene names: TFB5, YDR079C-A
Sequence domains: Transcription factor TFIIH complex subunit Tfb5
General transcription and DNA repair factor IIH subunit SSL1 Chain: 6
Molecule details ›
Chain: 6
Length: 461 amino acids
Theoretical weight: 51.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q04673 (Residues: 1-461; Coverage: 96%)
Gene names: SSL1, YLR005W
Sequence domains:
General transcription and DNA repair factor IIH helicase subunit XPB Chain: 7
Molecule details ›
Chain: 7
Length: 843 amino acids
Theoretical weight: 94.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q00578 (Residues: 1-843; Coverage: 95%)
Gene names: LOM3, RAD25, SSL2, UVS112, YIL143C
Sequence domains:
Unknown protein Chain: Z
Molecule details ›
Chain: Z
Length: 43 amino acids
Theoretical weight: 3.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
NONTEMPLATE DNA Chain: N
Molecule details ›
Chain: N
Length: 106 nucleotides
Theoretical weight: 32.72 KDa
TEMPLATE DNA Chain: T
Molecule details ›
Chain: T
Length: 106 nucleotides
Theoretical weight: 32.68 KDa

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.7Å
Relevant EMDB volumes: EMD-3846
Expression systems:
  • Escherichia coli BL21(DE3)
  • Trichoplusia ni