› 7emf

Electron Microscopy
3.5Å resolution

Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation

Released:
DOI: 10.2210/pdb7emf/pdb
PDB entry 7emf coloured by chain, front view.
PDB entry 7emf coloured by chain, side view.
PDB entry 7emf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of the human Mediator and Mediator-bound preinitiation complex.
Chen X, Yin X, Li J, Wu Z, Qi Y, Wang X, Liu W, Xu Y
Science 372 (2021)
PMID: 33958484
Related structures: EMD-31191

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
PDBe Complex ID:
PDB-CPX-499043 (preferred)
Entry contents:
27 distinct polypeptide molecules
Macromolecules (27 distinct):
Mediator of RNA polymerase II transcription subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 1581 amino acids
Theoretical weight: 168.7 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15648 (Residues: 1-1581; Coverage: 100%)
Gene names: ARC205, CRSP1, CRSP200, DRIP205, DRIP230, MED1, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2
Sequence domains: Mediator of RNA polymerase II transcription subunit 1
Unknown Chain (poly A) Chain: B
Molecule details ›
Chain: B
Length: 20 amino acids
Theoretical weight: 1.44 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Mediator of RNA polymerase II transcription subunit 4 Chain: D
Molecule details ›
Chain: D
Length: 270 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NPJ6 (Residues: 1-270; Coverage: 100%)
Gene names: ARC36, DRIP36, HSPC126, MED4, VDRIP
Sequence domains: Vitamin-D-receptor interacting Mediator subunit 4
Mediator of RNA polymerase II transcription subunit 6 Chain: F
Molecule details ›
Chain: F
Length: 246 amino acids
Theoretical weight: 28.46 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75586 (Residues: 1-246; Coverage: 100%)
Gene names: ARC33, MED6
Sequence domains: MED6 mediator sub complex component
Mediator of RNA polymerase II transcription subunit 7 Chain: G
Molecule details ›
Chain: G
Length: 233 amino acids
Theoretical weight: 27.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43513 (Residues: 1-233; Coverage: 100%)
Gene names: ARC34, CRSP9, MED7
Sequence domains: MED7 protein
Mediator of RNA polymerase II transcription subunit 8 Chain: H
Molecule details ›
Chain: H
Length: 268 amino acids
Theoretical weight: 29.11 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q96G25 (Residues: 1-268; Coverage: 100%)
Gene name: MED8
Sequence domains: Mediator of RNA polymerase II transcription complex subunit 8
Mediator of RNA polymerase II transcription subunit 9 Chain: I
Molecule details ›
Chain: I
Length: 146 amino acids
Theoretical weight: 16.42 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NWA0 (Residues: 1-146; Coverage: 100%)
Gene names: MED25, MED9
Sequence domains: RNA polymerase II transcription mediator complex subunit 9
Mediator of RNA polymerase II transcription subunit 10 Chain: J
Molecule details ›
Chain: J
Length: 135 amino acids
Theoretical weight: 15.71 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9BTT4 (Residues: 1-135; Coverage: 100%)
Gene names: L6, MED10, TRG17, TRG20
Sequence domains: Transcription factor subunit Med10 of Mediator complex
Mediator of RNA polymerase II transcription subunit 11 Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9P086 (Residues: 1-117; Coverage: 100%)
Gene names: HSPC296, MED11
Sequence domains: Mediator complex protein
Mediator of RNA polymerase II transcription subunit 14 Chain: N
Molecule details ›
Chain: N
Length: 1454 amino acids
Theoretical weight: 160.79 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O60244 (Residues: 1-1454; Coverage: 100%)
Gene names: ARC150, CRSP2, CXorf4, DRIP150, EXLM1, MED14, RGR1, TRAP170
Sequence domains:
Mediator of RNA polymerase II transcription subunit 15 Chain: O
Molecule details ›
Chain: O
Length: 788 amino acids
Theoretical weight: 86.83 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q96RN5 (Residues: 1-788; Coverage: 100%)
Gene names: ARC105, CTG7A, MED15, PCQAP, TIG1, TNRC7
Sequence domains:
Mediator of RNA polymerase II transcription subunit 16 Chain: P
Molecule details ›
Chain: P
Length: 841 amino acids
Theoretical weight: 93.14 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9Y2X0 (Residues: 1-828; Coverage: 94%)
  • Best match: Q9Y2X0-2 (Residues: 1-841)
Gene names: DRIP92, MED16, THRAP5
Sequence domains:
Mediator of RNA polymerase II transcription subunit 17 Chain: Q
Molecule details ›
Chain: Q
Length: 651 amino acids
Theoretical weight: 72.98 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NVC6 (Residues: 1-651; Coverage: 100%)
Gene names: ARC77, CRSP6, DRIP77, DRIP80, MED17, TRAP80
Sequence domains: Subunit 17 of Mediator complex
Mediator of RNA polymerase II transcription subunit 18 Chain: R
Molecule details ›
Chain: R
Length: 208 amino acids
Theoretical weight: 23.69 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9BUE0 (Residues: 1-208; Coverage: 100%)
Gene name: MED18
Sequence domains: Med18 protein
Mediator of RNA polymerase II transcription subunit 19 Chain: S
Molecule details ›
Chain: S
Length: 244 amino acids
Theoretical weight: 26.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: A0JLT2 (Residues: 1-244; Coverage: 100%)
Gene names: LCMR1, MED19
Sequence domains: Mediator of RNA pol II transcription subunit 19
Mediator of RNA polymerase II transcription subunit 20 Chain: T
Molecule details ›
Chain: T
Length: 212 amino acids
Theoretical weight: 23.24 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9H944 (Residues: 1-212; Coverage: 100%)
Gene names: MED20, TRFP
Sequence domains: TATA-binding related factor (TRF) of subunit 20 of Mediator complex
Mediator of RNA polymerase II transcription subunit 21 Chain: U
Molecule details ›
Chain: U
Length: 144 amino acids
Theoretical weight: 15.58 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13503 (Residues: 1-144; Coverage: 100%)
Gene names: MED21, SRB7, SURB7
Sequence domains: Subunit 21 of Mediator complex
Mediator of RNA polymerase II transcription subunit 22 Chain: V
Molecule details ›
Chain: V
Length: 200 amino acids
Theoretical weight: 22.24 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15528 (Residues: 1-200; Coverage: 100%)
Gene names: MED22, SURF5
Sequence domains: Surfeit locus protein 5 subunit 22 of Mediator complex
Mediator of RNA polymerase II transcription subunit 23 Chain: W
Molecule details ›
Chain: W
Length: 1368 amino acids
Theoretical weight: 156.65 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9ULK4 (Residues: 1-1368; Coverage: 100%)
Gene names: ARC130, CRSP3, DRIP130, KIAA1216, MED23, SUR2
Sequence domains: Mediator complex subunit 23
Mediator of RNA polymerase II transcription subunit 24 Chain: X
Molecule details ›
Chain: X
Length: 989 amino acids
Theoretical weight: 110.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75448 (Residues: 1-989; Coverage: 100%)
Gene names: ARC100, CRSP4, DRIP100, KIAA0130, MED24, THRAP4, TRAP100
Sequence domains: Mediator complex subunit 24 N-terminal
Mediator of RNA polymerase II transcription subunit 25 Chain: Y
Molecule details ›
Chain: Y
Length: 747 amino acids
Theoretical weight: 78.23 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q71SY5 (Residues: 1-747; Coverage: 100%)
Gene names: ACID1, ARC92, MED25, PTOV2, TCBAP0758
Sequence domains:
Mediator of RNA polymerase II transcription subunit 26 Chain: Z
Molecule details ›
Chain: Z
Length: 600 amino acids
Theoretical weight: 65.54 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O95402 (Residues: 1-600; Coverage: 100%)
Gene names: ARC70, CRSP7, MED26
Sequence domains:
Mediator of RNA polymerase II transcription subunit 27 Chain: 0
Molecule details ›
Chain: 0
Length: 311 amino acids
Theoretical weight: 35.48 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6P2C8 (Residues: 1-311; Coverage: 100%)
Gene names: CRSP34, CRSP8, MED27
Sequence domains: Mediator complex subunit 27
Mediator of RNA polymerase II transcription subunit 28 Chain: 1
Molecule details ›
Chain: 1
Length: 178 amino acids
Theoretical weight: 19.54 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9H204 (Residues: 1-178; Coverage: 100%)
Gene names: EG1, FKSG20, MED28
Sequence domains: Mediator complex subunit 28
Mediator of RNA polymerase II transcription subunit 29 Chain: 2
Molecule details ›
Chain: 2
Length: 200 amino acids
Theoretical weight: 21.09 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NX70 (Residues: 1-200; Coverage: 100%)
Gene names: IXL, MED29
Sequence domains: Mediator complex subunit 29
Mediator of RNA polymerase II transcription subunit 30 Chain: 3
Molecule details ›
Chain: 3
Length: 178 amino acids
Theoretical weight: 20.3 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q96HR3 (Residues: 1-178; Coverage: 100%)
Gene names: MED30, THRAP6, TRAP25
Sequence domains: Mediator complex subunit 30
Mediator of RNA polymerase II transcription subunit 31 Chain: 4
Molecule details ›
Chain: 4
Length: 131 amino acids
Theoretical weight: 15.83 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9Y3C7 (Residues: 1-131; Coverage: 100%)
Gene names: CGI-125, MED31, SOH1
Sequence domains: SOH1

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-31191
Expression system: Homo sapiens

Quick links

Citations

13 review citations

The Mediator complex as a master regulator of transcription by RNA polymerase II.
Richter et al. (2022)
12 more

3 mentions without citation

Assembly of RNA polymerase II transcription initiation complexes.
Farnung et al. (2022)
2 more