› 5ip7

X-ray diffraction
3.52Å resolution

Structure of RNA Polymerase II-Tfg1 peptide complex

Released:
DOI: 10.2210/pdb5ip7/pdb
PDB entry 5ip7 coloured by chain, front view.
PDB entry 5ip7 coloured by chain, side view.
PDB entry 5ip7 coloured by chain, top view.
Source organisms:
Primary publication:
Transcription initiation complex structures elucidate DNA opening.
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature 533 353-8 (2016)
PMID: 27193681

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137348 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1732 amino acids
Theoretical weight: 191.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04050 (Residues: 2-1733; 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: 1223 amino acids
Theoretical weight: 138.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08518 (Residues: 2-1224; 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:
Structure 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
Structure domains: Growth Hormone; Chain: A;
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:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 87 amino acids
Theoretical weight: 10.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20435 (Residues: 69-155; Coverage: 56%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
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:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 145 amino acids
Theoretical weight: 16.39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20436 (Residues: 2-146; Coverage: 99%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
Structure domains: Nucleic acid-binding proteins
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:
Structure domains: N-terminal domain of TfIIb
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
Structure domains: Homeodomain-like
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:
Structure domains: RNA polymerase, RBP11-like subunit
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 S288C
UniProt:
  • Canonical: P40422 (Residues: 25-70; Coverage: 66%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
Transcription initiation factor IIF subunit alpha Chain: Q
Molecule details ›
Chain: Q
Length: 15 amino acids
Theoretical weight: 2.1 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
UniProt:
  • Canonical: P41895 (Residues: 21-35; Coverage: 2%)
Gene names: G7526, SSU71, TFG1, YGR186W

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2221
Unit cell:
a: 221.22Å b: 392.73Å c: 282.19Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.154 0.18
Expression system: Not provided

Quick links

Citations

43 review citations

Eukaryotic core promoters and the functional basis of transcription initiation.
Haberle et al. (2018)
42 more