› 3rj1

X-ray diffraction
4.3Å resolution

Architecture of the Mediator Head module

Released:
DOI: 10.2210/pdb3rj1/pdb
PDB entry 3rj1 coloured by chain, front view.
PDB entry 3rj1 coloured by chain, side view.
PDB entry 3rj1 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Architecture of the Mediator head module.
Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y
Nature 475 240-3 (2011)
PMID: 21725323

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152365 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
Mediator of RNA polymerase II transcription subunit 11 Chains: A, H, O
Molecule details ›
Chains: A, H, O
Length: 131 amino acids
Theoretical weight: 15.24 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q99278 (Residues: 1-115; Coverage: 100%)
Gene names: MED11, YM9718.11C, YMR112C
Sequence domains: Mediator complex protein
Mediator of RNA polymerase II transcription subunit 17 Chains: B, I, P
Molecule details ›
Chains: B, I, P
Length: 583 amino acids
Theoretical weight: 66.91 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32569 (Residues: 109-687; Coverage: 83%)
Gene names: MED17, SRB4, YER022W
Sequence domains: Subunit 17 of Mediator complex
Mediator of RNA polymerase II transcription subunit 8 Chains: C, J, Q
Molecule details ›
Chains: C, J, Q
Length: 223 amino acids
Theoretical weight: 25.48 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P38304 (Residues: 1-223; Coverage: 100%)
Gene names: MED8, YBR1403, YBR193C
Sequence domains: Mediator of RNA polymerase II transcription complex subunit 8
Mediator of RNA polymerase II transcription subunit 22 Chains: D, K, R
Molecule details ›
Chains: D, K, R
Length: 121 amino acids
Theoretical weight: 14.11 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32570 (Residues: 1-121; Coverage: 100%)
Gene names: MED22, SRB6, YBR1721, YBR253W
Sequence domains: Surfeit locus protein 5 subunit 22 of Mediator complex
Mediator of RNA polymerase II transcription subunit 18 Chains: E, L, S
Molecule details ›
Chains: E, L, S
Length: 275 amino acids
Theoretical weight: 31.13 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32585 (Residues: 1-307; Coverage: 90%)
Gene names: MED18, SRB5, YGR104C
Sequence domains: Med18 protein
Mediator of RNA polymerase II transcription subunit 20 Chains: F, M, T
Molecule details ›
Chains: F, M, T
Length: 210 amino acids
Theoretical weight: 23.11 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P34162 (Residues: 1-210; Coverage: 100%)
Gene names: HRS2, MED20, SRB2, YHR041C
Sequence domains: TATA-binding related factor (TRF) of subunit 20 of Mediator complex
Mediator of RNA polymerase II transcription subunit 6 Chains: G, N, U
Molecule details ›
Chains: G, N, U
Length: 295 amino acids
Theoretical weight: 33.5 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P38782 (Residues: 1-295; Coverage: 100%)
Gene names: MED6, MTR32, YHR058C
Sequence domains: MED6 mediator sub complex component

Ligands and Environments

1 bound ligand:
Ligand SE 98 x SE
1 modified residue:
Ligand MSE 156 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P3221
Unit cell:
a: 265.914Å b: 265.914Å c: 319.948Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.348 0.345 0.373
Expression system: Trichoplusia ni

Quick links

Citations

27 review citations

The Mediator complex: a central integrator of transcription.
Allen et al. (2015)
26 more

6 mentions without citation

Role of integrative structural biology in understanding transcriptional initiation.
Trnka et al. (2019)
5 more