› 5u0s

Electron Microscopy
7.8Å resolution

Cryo-EM structure of the Mediator-RNAPII complex

Released:
DOI: 10.2210/pdb5u0s/pdb
PDB entry 5u0s coloured by chain, front view.
PDB entry 5u0s coloured by chain, side view.
PDB entry 5u0s 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-8480

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 28-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126927 (preferred)
Entry contents:
28 distinct polypeptide molecules
Macromolecules (28 distinct):
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 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 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 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 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 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
DNA-directed RNA polymerase II subunit rpb1 Chain: a
Molecule details ›
Chain: a
Length: 1752 amino acids
Theoretical weight: 194.37 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P36594 (Residues: 1-1752; Coverage: 100%)
Gene names: SPBC28F2.12, rpb1
Sequence domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: b
Molecule details ›
Chain: b
Length: 1210 amino acids
Theoretical weight: 138.03 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q02061 (Residues: 1-1210; Coverage: 100%)
Gene names: SPAC23G3.01, SPAC521.06, rpb2
Sequence domains:
DNA-directed RNA polymerase II subunit RPB3 Chain: c
Molecule details ›
Chain: c
Length: 297 amino acids
Theoretical weight: 33.75 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P37382 (Residues: 1-297; Coverage: 100%)
Gene names: SPCC1442.10c, rpb3
Sequence domains:
DNA-directed RNA polymerase II subunit rpb4 Chain: d
Molecule details ›
Chain: d
Length: 135 amino acids
Theoretical weight: 15.38 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74825 (Residues: 1-135; Coverage: 100%)
Gene names: SPBC337.14, rpb4
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: e
Molecule details ›
Chain: e
Length: 210 amino acids
Theoretical weight: 23.95 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q09191 (Residues: 1-210; Coverage: 100%)
Gene names: SPAC23C4.15, rpb5
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: f
Molecule details ›
Chain: f
Length: 142 amino acids
Theoretical weight: 15.74 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P36595 (Residues: 1-142; Coverage: 100%)
Gene names: SPCC1020.04c, rpb6, rpo15
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase II subunit rpb7 Chain: g
Molecule details ›
Chain: g
Length: 172 amino acids
Theoretical weight: 19.12 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O14459 (Residues: 1-172; Coverage: 100%)
Gene names: SPACUNK4.06c, SPAPYUK71.02, rpb7
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: h
Molecule details ›
Chain: h
Length: 125 amino acids
Theoretical weight: 14.32 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q92399 (Residues: 1-125; Coverage: 100%)
Gene names: SPBC14C8.12, rpb8
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: i
Molecule details ›
Chain: i
Length: 113 amino acids
Theoretical weight: 13.19 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74635 (Residues: 1-113; Coverage: 100%)
Gene names: SPAPYUG7.04c, rpb9
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: j
Molecule details ›
Chain: j
Length: 71 amino acids
Theoretical weight: 8.29 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O13877 (Residues: 1-71; Coverage: 100%)
Gene names: SPAC1B3.12c, rpb10
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase II subunit RPB11 Chain: k
Molecule details ›
Chain: k
Length: 123 amino acids
Theoretical weight: 14.14 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P87123 (Residues: 1-123; Coverage: 100%)
Gene names: SPAC3A12.07, rpb11
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: l
Molecule details ›
Chain: l
Length: 63 amino acids
Theoretical weight: 7.22 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P48011 (Residues: 1-63; Coverage: 100%)
Gene names: SPBC19C2.03, rpb12, rpc10
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7.8Å
Relevant EMDB volumes: EMD-8480

Quick links

Citations

28 review citations

Organization and regulation of gene transcription.
Cramer P. (2019)
27 more

6 mentions without citation

The complex structure and function of Mediator.
Harper et al. (2018)
5 more