› 5u0p

Electron Microscopy
4.4Å resolution

Cryo-EM structure of the transcriptional Mediator

Released:
DOI: 10.2210/pdb5u0p/pdb
PDB entry 5u0p coloured by chain, front view.
PDB entry 5u0p coloured by chain, side view.
PDB entry 5u0p coloured by chain, top view.
Source organism: Schizosaccharomyces pombe
Primary publication:
Mediator structure and rearrangements required for holoenzyme formation.
Tsai KL, Yu X, Gopalan S, Chao TC, Zhang Y, Florens L, Washburn MP, Murakami K, Conaway RC, Conaway JW, Asturias FJ
Nature 544 196-201 (2017)
PMID: 28241144
Related structures: EMD-8479

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-126936 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
Mediator of RNA polymerase II transcription subunit 14 Chain: N
Molecule details ›
Chain: N
Length: 931 amino acids
Theoretical weight: 105.38 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9P7Y4 (Residues: 1-879; Coverage: 100%)
Gene names: SPBC1A4.10c, SPBP23A10.01c, med14, pmc1
Sequence domains: Mediator complex subunit MED14
Mediator of RNA polymerase II transcription subunit 6 Chain: F
Molecule details ›
Chain: F
Length: 216 amino acids
Theoretical weight: 24.93 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9US45 (Residues: 1-216; Coverage: 100%)
Gene names: SPAC1002.15c, med6, pmc5
Sequence domains: MED6 mediator sub complex component
Mediator of RNA polymerase II transcription subunit 8 Chain: H
Molecule details ›
Chain: H
Length: 200 amino acids
Theoretical weight: 23.36 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94646 (Residues: 1-200; Coverage: 100%)
Gene names: SPBC21.04, med8, sep15
Sequence domains: Mediator of RNA polymerase II transcription complex subunit 8
Mediator of RNA polymerase II transcription subunit 17 Chain: Q
Molecule details ›
Chain: Q
Length: 545 amino acids
Theoretical weight: 62.55 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P87306 (Residues: 1-545; Coverage: 100%)
Gene names: SPBC31F10.04c, med17, srb4
Sequence domains: Subunit 17 of Mediator complex
Mediator of RNA polymerase II transcription subunit 18 Chain: R
Molecule details ›
Chain: R
Length: 207 amino acids
Theoretical weight: 24.06 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O14198 (Residues: 1-207; Coverage: 100%)
Gene names: SPAC5D6.05, med18, pmc6, sep11
Sequence domains: Med18 protein
Mediator of RNA polymerase II transcription subunit 20 Chain: T
Molecule details ›
Chain: T
Length: 193 amino acids
Theoretical weight: 22.37 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q10317 (Residues: 1-193; Coverage: 100%)
Gene names: SPAC17G8.05, med20
Sequence domains: TATA-binding related factor (TRF) of subunit 20 of Mediator complex
Mediator of RNA polymerase II transcription subunit 11 Chain: K
Molecule details ›
Chain: K
Length: 116 amino acids
Theoretical weight: 13.12 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9P6Q0 (Residues: 1-112; Coverage: 100%)
Gene names: SPAC644.10, med11
Sequence domains: Mediator complex protein
Mediator of RNA polymerase II transcription subunit 22 Chain: V
Molecule details ›
Chain: V
Length: 136 amino acids
Theoretical weight: 15.4 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O14010 (Residues: 1-136; Coverage: 100%)
Gene names: SPAC29A4.07, med22, srb6
Sequence domains: Surfeit locus protein 5 subunit 22 of Mediator complex
Mediator complex subunit 4 Chain: D
Molecule details ›
Chain: D
Length: 239 amino acids
Theoretical weight: 20.36 KDa
Source organism: Schizosaccharomyces pombe
Mediator of RNA polymerase II transcription subunit 7 Chain: G
Molecule details ›
Chain: G
Length: 376 amino acids
Theoretical weight: 43.57 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O60104 (Residues: 1-376; Coverage: 100%)
Gene names: SPBC14F5.08, med7
Sequence domains: MED7 protein
Mediator of RNA polymerase II transcription subunit 21 Chain: U
Molecule details ›
Chain: U
Length: 138 amino acids
Theoretical weight: 15.82 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94376 (Residues: 1-138; Coverage: 100%)
Gene names: SPBC1604.10, med21, srb7
Sequence domains: Subunit 21 of Mediator complex
Mediator of RNA polymerase II transcription subunit 31 Chain: 3
Molecule details ›
Chain: 3
Length: 139 amino acids
Theoretical weight: 16.91 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9USH1 (Residues: 1-139; Coverage: 100%)
Gene names: SPCP31B10.03c, med31, sep10
Sequence domains: SOH1
Mediator complex subunit 9 Chain: I
Molecule details ›
Chain: I
Length: 121 amino acids
Theoretical weight: 13.81 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O13964 (Residues: 1-121; Coverage: 100%)
Gene name: SPAC24C9.04
Mediator of RNA polymerase II transcription subunit 27 Chain: 2
Molecule details ›
Chain: 2
Length: 273 amino acids
Theoretical weight: 31.13 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q10477 (Residues: 1-273; Coverage: 100%)
Gene names: SPAC17C9.05c, med27, pmc3
Sequence domains: Mediator complex subunit 27
Mediator complex subunit 19 Chain: S
Molecule details ›
Chain: S
Length: 139 amino acids
Theoretical weight: 11.85 KDa
Source organism: Schizosaccharomyces pombe
Mediator complex subunit 10 Chain: J
Molecule details ›
Chain: J
Length: 132 amino acids
Theoretical weight: 11.25 KDa
Source organism: Schizosaccharomyces pombe

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-8479

Quick links

Citations

30 review citations

Transcription regulation by the Mediator complex.
Soutourina J. (2018)
29 more

5 mentions without citation

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.
El Khattabi et al. (2019)
4 more