5fmf

Electron Microscopy
6Å resolution

the P-lobe of RNA polymerase II pre-initiation complex

Released:
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of an RNA polymerase II preinitiation complex.
Proc. Natl. Acad. Sci. U.S.A. 112 13543-8 (2015)
PMID: 26483468
Related structures: EMD-3114

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
Entry contents:
25 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (27 distinct):
General transcription and DNA repair factor IIH helicase subunit XPB Chain: 1
Molecule details ›
Chain: 1
Length: 492 amino acids
Theoretical weight: 56.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q00578 (Residues: 294-785; Coverage: 58%)
Gene names: LOM3, RAD25, SSL2, UVS112, YIL143C
Sequence domains: Type III restriction enzyme, res subunit
Transcription elongation factor S-II Chain: 2
Molecule details ›
Chain: 2
Length: 174 amino acids
Theoretical weight: 19.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07273 (Residues: 136-309; Coverage: 56%)
Gene names: DST1, PPR2, YGL043W
Sequence domains:
DNA-directed RNA polymerase II subunit RPB1 Chain: A
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: 266 amino acids
Theoretical weight: 29.92 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P16370 (Residues: 3-268; Coverage: 84%)
Gene names: RPB3, YIL021W
Sequence domains:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 178 amino acids
Theoretical weight: 20.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20433 (Residues: 3-221; Coverage: 81%)
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: 214 amino acids
Theoretical weight: 24.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20434 (Residues: 2-215; 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: 84 amino acids
Theoretical weight: 9.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20435 (Residues: 72-155; Coverage: 54%)
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
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
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: 119 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P27999 (Residues: 2-120; Coverage: 98%)
Gene names: RPB9, YGL070C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 65 amino acids
Theoretical weight: 7.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22139 (Residues: 1-65; Coverage: 93%)
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: 115 amino acids
Theoretical weight: 13.11 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38902 (Residues: 1-115; Coverage: 96%)
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: 46 amino acids
Theoretical weight: 5.25 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40422 (Residues: 25-70; Coverage: 66%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription initiation factor IIA large subunit Chain: M
Molecule details ›
Chain: M
Length: 116 amino acids
Theoretical weight: 13.59 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32773 (Residues: 2-286; Coverage: 41%)
Gene names: TOA1, YOR194C
Transcription initiation factor IIA subunit 2 Chain: O
Molecule details ›
Chain: O
Length: 122 amino acids
Theoretical weight: 13.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32774 (Residues: 1-122; Coverage: 100%)
Gene names: TOA2, YKL058W
Sequence domains:
Transcription initiation factor IIB Chain: P
Molecule details ›
Chain: P
Length: 345 amino acids
Theoretical weight: 38.26 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P29055 (Residues: 1-345; Coverage: 100%)
Gene names: P9513.4, SUA7, YPR086W
Sequence domains:
TATA-box-binding protein Chain: Q
Molecule details ›
Chain: Q
Length: 180 amino acids
Theoretical weight: 20.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P13393 (Residues: 61-240; Coverage: 75%)
Gene names: BTF1, SPT15, TBP1, YER148W
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
Transcription initiation factor IIE subunit alpha Chain: R
Molecule details ›
Chain: R
Length: 160 amino acids
Theoretical weight: 18.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36100 (Residues: 1-160; Coverage: 33%)
Gene names: TFA1, YKL028W
Sequence domains: TFIIE alpha subunit
Transcription initiation factor IIE subunit beta Chain: S
Molecule details ›
Chain: S
Length: 123 amino acids
Theoretical weight: 14.52 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36145 (Residues: 125-247; Coverage: 38%)
Gene names: TFA2, YKR062W
Sequence domains: TFA2 Winged helix domain 2
Transcription initiation factor IIF subunit alpha Chain: U
Molecule details ›
Chain: U
Length: 150 amino acids
Theoretical weight: 17.71 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41895 (Residues: 94-417; Coverage: 20%)
Gene names: G7526, SSU71, TFG1, YGR186W
Transcription initiation factor IIF subunit beta Chain: V
Molecule details ›
Chain: V
Length: 174 amino acids
Theoretical weight: 20.71 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41896 (Residues: 54-359; Coverage: 44%)
Gene names: TFG2, YGR005C
Sequence domains:
General transcription and DNA repair factor IIH subunit TFB2 Chain: W
Molecule details ›
Chain: W
Length: 62 amino acids
Theoretical weight: 7.34 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02939 (Residues: 447-508; Coverage: 12%)
Gene names: TFB2, YPL122C
General transcription and DNA repair factor IIH subunit TFB5 Chain: X
Molecule details ›
Chain: X
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E7C1 (Residues: 2-64; Coverage: 88%)
Gene names: TFB5, YDR079C-A
General transcription and DNA repair factor IIH helicase subunit XPD Chain: Y
Molecule details ›
Chain: Y
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:
NON-TEMPLATE STRAND DNA Chain: N
Molecule details ›
Chain: N
Length: 72 nucleotides
Theoretical weight: 22.48 KDa
TEMPLATE STRAND DNA Chain: T
Molecule details ›
Chain: T
Length: 72 nucleotides
Theoretical weight: 21.91 KDa

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution:
Relevant EMDB volumes: EMD-3114