› 8uoq

Electron Microscopy
3.8Å resolution

Composite map of PIC_delta_TFIIK form2

Released:
DOI: 10.2210/pdb8uoq/pdb
PDB entry 8uoq coloured by chain, front view.
PDB entry 8uoq coloured by chain, side view.
PDB entry 8uoq coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3.
Yang C, Basnet P, Sharmin S, Shen H, Kaplan CD, Murakami K
Nucleic Acids Res (2024)
PMID: 39287137
Related structures: EMD-42437

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-513327 (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (30 distinct):
Transcription initiation factor IIB Chain: M
Molecule details ›
Chain: M
Length: 345 amino acids
Theoretical weight: 38.26 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P29055 (Residues: 1-345; Coverage: 100%)
Gene names: P9513.4, SUA7, YPR086W
Sequence domains:
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1733 amino acids
Theoretical weight: 191.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04050 (Residues: 1-1733; Coverage: 100%)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
Sequence domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1224 amino acids
Theoretical weight: 138.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08518 (Residues: 1-1224; Coverage: 100%)
Gene names: RPB150, RPB2, RPO22, YOR151C
Sequence domains:
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
UniProt:
  • Canonical: P16370 (Residues: 1-318; Coverage: 100%)
Gene names: RPB3, YIL021W
Sequence domains:
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
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
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
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
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
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
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
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
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 IIF subunit alpha Chain: Q
Molecule details ›
Chain: Q
Length: 735 amino acids
Theoretical weight: 82.32 KDa
Source organism: Saccharomyces cerevisiae
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: P
Molecule details ›
Chain: P
Length: 400 amino acids
Theoretical weight: 46.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41896 (Residues: 1-400; Coverage: 100%)
Gene names: TFG2, YGR005C
Sequence domains:
Transcription elongation factor S-II Chain: S
Molecule details ›
Chain: S
Length: 309 amino acids
Theoretical weight: 34.9 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P07273 (Residues: 1-309; Coverage: 100%)
Gene names: DST1, PPR2, YGL043W
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
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
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 IIA large subunit Chain: U
Molecule details ›
Chain: U
Length: 286 amino acids
Theoretical weight: 32.23 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
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
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
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: 482 amino acids
Theoretical weight: 54.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36100 (Residues: 1-482; Coverage: 100%)
Gene names: TFA1, YKL028W
Sequence domains: TFIIE alpha subunit
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
UniProt:
  • Canonical: P36145 (Residues: 1-328; Coverage: 100%)
Gene names: TFA2, YKR062W
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
UniProt:
  • Canonical: P20433 (Residues: 1-221; Coverage: 100%)
Gene names: J0654, RPB4, YJL140W
Sequence domains: RNA polymerase Rpb4
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
UniProt:
  • Canonical: P34087 (Residues: 1-171; Coverage: 100%)
Gene names: D9509.22, RPB7, YDR404C
Sequence domains:
General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 Chain: 0
Molecule details ›
Chain: 0
Length: 778 amino acids
Theoretical weight: 89.9 KDa
Source organism: Saccharomyces cerevisiae
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: 642 amino acids
Theoretical weight: 72.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32776 (Residues: 1-642; Coverage: 100%)
Gene names: D9740.3, TFB1, YDR311W
Sequence domains:
General transcription and DNA repair factor IIH subunit TFB4 Chain: 4
Molecule details ›
Chain: 4
Length: 338 amino acids
Theoretical weight: 37.51 KDa
Source organism: Saccharomyces cerevisiae
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 SSL1 Chain: 6
Molecule details ›
Chain: 6
Length: 461 amino acids
Theoretical weight: 52.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04673 (Residues: 1-461; Coverage: 100%)
Gene names: SSL1, YLR005W
Sequence domains:
General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 Chain: 7
Molecule details ›
Chain: 7
Length: 843 amino acids
Theoretical weight: 95.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q00578 (Residues: 1-843; Coverage: 100%)
Gene names: LOM3, RAD25, SSL2, UVS112, YIL143C
Sequence domains:
General transcription and DNA repair factor IIH subunit TFB2 Chain: 2
Molecule details ›
Chain: 2
Length: 513 amino acids
Theoretical weight: 58.6 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02939 (Residues: 1-513; Coverage: 100%)
Gene names: TFB2, YPL122C
Sequence domains:
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
UniProt:
  • Canonical: Q3E7C1 (Residues: 1-72; Coverage: 100%)
Gene names: TFB5, YDR079C-A
Sequence domains: Transcription factor TFIIH complex subunit Tfb5
non-template strand Chain: N
Molecule details ›
Chain: N
Length: 64 nucleotides
Theoretical weight: 19.7 KDa
template strand Chain: T
Molecule details ›
Chain: T
Length: 64 nucleotides
Theoretical weight: 19.72 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 15 x ZN
Ligand MG 2 x MG
Ligand SF4 1 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-42437
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links