› 8tqw

Electron Microscopy
8.2Å resolution

Structure of human transcriptional Mediator complex

Released:
DOI: 10.2210/pdb8tqw/pdb
PDB entry 8tqw coloured by chain, front view.
PDB entry 8tqw coloured by chain, side view.
PDB entry 8tqw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module.
Chao TC, Chen SF, Kim HJ, Tang HC, Tseng HC, Xu A, Palao L, Khadka S, Li T, Huang MF, Lee DF, Murakami K, Boyer TG, Tsai KL
Mol Cell (2024)
PMID: 39321804
Related structures: EMD-41565

Function and Biology Details

Reactions catalysed: 
ATP + a protein = ADP + a phosphoprotein
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 29-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-252173 (preferred)
Entry contents:
29 distinct polypeptide molecules
Macromolecules (29 distinct):
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
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
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
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
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
UniProt:
  • Canonical: Q9Y3C7 (Residues: 1-131; Coverage: 100%)
Gene names: CGI-125, MED31, SOH1
Sequence domains: SOH1
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
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 Chain: B
Molecule details ›
Chain: B
Length: 20 amino acids
Theoretical weight: 1.72 KDa
Source organism: 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
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
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
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
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
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
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
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
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
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: 877 amino acids
Theoretical weight: 96.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2X0 (Residues: 1-877; Coverage: 100%)
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
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
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
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
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
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
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
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
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
Cyclin-dependent kinase 8 Chain: a
Molecule details ›
Chain: a
Length: 464 amino acids
Theoretical weight: 53.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49336 (Residues: 1-464; Coverage: 100%)
Gene name: CDK8
Sequence domains: Protein kinase domain
Cyclin-C Chain: b
Molecule details ›
Chain: b
Length: 283 amino acids
Theoretical weight: 33.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P24863 (Residues: 1-283; Coverage: 100%)
Gene name: CCNC
Sequence domains:
Mediator of RNA polymerase II transcription subunit 12 Chain: c
Molecule details ›
Chain: c
Length: 2177 amino acids
Theoretical weight: 243.35 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q93074 (Residues: 1-2177; Coverage: 100%)
  • Best match: Q93074-2 (Residues: 1-2180)
Gene names: ARC240, CAGH45, HOPA, KIAA0192, MED12, TNRC11, TRAP230
Sequence domains:
Mediator of RNA polymerase II transcription subunit 13 Chain: d
Molecule details ›
Chain: d
Length: 2174 amino acids
Theoretical weight: 239.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UHV7 (Residues: 1-2174; Coverage: 100%)
Gene names: ARC250, KIAA0593, MED13, THRAP1, TRAP240
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 8.2Å
Relevant EMDB volumes: EMD-41565

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