› 5sva

Electron Microscopy
15.3Å resolution

Mediator-RNA Polymerase II Pre-Initiation Complex

Released:
DOI: 10.2210/pdb5sva/pdb
PDB entry 5sva coloured by chain, front view.
PDB entry 5sva coloured by chain, side view.
PDB entry 5sva coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.
Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD
Cell 166 1411-1422.e16 (2016)
PMID: 27610567
Related structures: EMD-8305

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 40-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119121 (preferred)
Entry contents:
38 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (40 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1733 amino acids
Theoretical weight: 191.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04050 (Residues: 1-1733; Coverage: 100%)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
Sequence domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1224 amino acids
Theoretical weight: 138.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08518 (Residues: 1-1224; Coverage: 100%)
Gene names: RPB150, RPB2, RPO22, YOR151C
Sequence domains:
DNA-directed RNA polymerase II subunit RPB3 Chain: C
Molecule details ›
Chain: C
Length: 318 amino acids
Theoretical weight: 35.33 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P16370 (Residues: 1-318; Coverage: 100%)
Gene names: RPB3, YIL021W
Sequence domains:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20433 (Residues: 1-221; Coverage: 100%)
Gene names: J0654, RPB4, YJL140W
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P34087 (Residues: 1-171; Coverage: 100%)
Gene names: D9509.22, RPB7, YDR404C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P27999 (Residues: 1-122; Coverage: 100%)
Gene names: RPB9, YGL070C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Gene names: RPB10, YOR210W
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase II subunit RPB11 Chain: K
Molecule details ›
Chain: K
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Gene names: RPB11, YOL005C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Mediator of RNA polymerase II transcription subunit 6 Chain: M
Molecule details ›
Chain: M
Length: 295 amino acids
Theoretical weight: 32.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38782 (Residues: 1-295; Coverage: 100%)
Gene names: MED6, MTR32, YHR058C
Sequence domains: MED6 mediator sub complex component
Mediator of RNA polymerase II transcription subunit 8 Chain: N
Molecule details ›
Chain: N
Length: 223 amino acids
Theoretical weight: 25.3 KDa
Source organism: Saccharomyces cerevisiae
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 11 Chain: O
Molecule details ›
Chain: O
Length: 115 amino acids
Theoretical weight: 13.32 KDa
Source organism: Saccharomyces cerevisiae
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 Chain: P
Molecule details ›
Chain: P
Length: 687 amino acids
Theoretical weight: 78.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32569 (Residues: 1-687; Coverage: 100%)
Gene names: MED17, SRB4, YER022W
Sequence domains: Subunit 17 of Mediator complex
Mediator of RNA polymerase II transcription subunit 18 Chain: Q
Molecule details ›
Chain: Q
Length: 307 amino acids
Theoretical weight: 34.32 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32585 (Residues: 1-307; Coverage: 100%)
Gene names: MED18, SRB5, YGR104C
Sequence domains: Med18 protein
Mediator of RNA polymerase II transcription subunit 20 Chain: R
Molecule details ›
Chain: R
Length: 210 amino acids
Theoretical weight: 22.92 KDa
Source organism: Saccharomyces cerevisiae
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 22 Chain: S
Molecule details ›
Chain: S
Length: 121 amino acids
Theoretical weight: 13.88 KDa
Source organism: Saccharomyces cerevisiae
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 4 Chain: T
Molecule details ›
Chain: T
Length: 284 amino acids
Theoretical weight: 32.24 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12343 (Residues: 1-284; Coverage: 100%)
Gene names: MED4, O3630, YOR174W
Sequence domains: Vitamin-D-receptor interacting Mediator subunit 4
Mediator of RNA polymerase II transcription subunit 7 Chain: U
Molecule details ›
Chain: U
Length: 222 amino acids
Theoretical weight: 25.62 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08278 (Residues: 1-222; Coverage: 100%)
Gene names: MED7, YOL135C
Sequence domains: MED7 protein
Mediator of RNA polymerase II transcription subunit 9 Chain: V
Molecule details ›
Chain: V
Length: 149 amino acids
Theoretical weight: 17.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33308 (Residues: 1-149; Coverage: 100%)
Gene names: CSE2, MED9, N2046, YNR010W
Sequence domains: RNA polymerase II transcription mediator complex subunit 9
Mediator of RNA polymerase II transcription subunit 21 Chain: W
Molecule details ›
Chain: W
Length: 140 amino acids
Theoretical weight: 16.09 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P47822 (Residues: 1-140; Coverage: 100%)
Gene names: D9740.17, MED21, SRB7, YDR308C
Sequence domains: Subunit 21 of Mediator complex
Mediator of RNA polymerase II transcription subunit 31 Chain: X
Molecule details ›
Chain: X
Length: 127 amino acids
Theoretical weight: 14.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38633 (Residues: 1-127; Coverage: 100%)
Gene names: G2864, MED31, SOH1, YGL127C
Sequence domains: SOH1
General transcription and DNA repair factor IIH helicase subunit XPD Chain: Y
Molecule details ›
Chain: Y
Length: 778 amino acids
Theoretical weight: 89.9 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P06839 (Residues: 1-778; Coverage: 100%)
Gene names: RAD3, REM1, YER171W
Sequence domains:
General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 Chain: Z
Molecule details ›
Chain: Z
Length: 843 amino acids
Theoretical weight: 95.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q00578 (Residues: 1-843; Coverage: 100%)
Gene names: LOM3, RAD25, SSL2, UVS112, YIL143C
Sequence domains:
General transcription and DNA repair factor IIH subunit TFB2 Chain: a
Molecule details ›
Chain: a
Length: 513 amino acids
Theoretical weight: 58.6 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02939 (Residues: 1-513; Coverage: 100%)
Gene names: TFB2, YPL122C
Sequence domains:
General transcription and DNA repair factor IIH subunit TFB5 Chain: b
Molecule details ›
Chain: b
Length: 72 amino acids
Theoretical weight: 8.24 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E7C1 (Residues: 1-72; Coverage: 100%)
Gene names: TFB5, YDR079C-A
Sequence domains: Transcription factor TFIIH complex subunit Tfb5
Transcription initiation factor IIB Chain: c
Molecule details ›
Chain: c
Length: 345 amino acids
Theoretical weight: 38.26 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P29055 (Residues: 1-345; Coverage: 100%)
Gene names: P9513.4, SUA7, YPR086W
Sequence domains:
Transcription initiation factor IIA large subunit Chain: d
Molecule details ›
Chain: d
Length: 286 amino acids
Theoretical weight: 32.23 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P32773 (Residues: 1-286; Coverage: 100%)
Gene names: TOA1, YOR194C
Sequence domains: Transcription factor IIA, alpha/beta subunit
Transcription initiation factor IIA subunit 2 Chain: e
Molecule details ›
Chain: e
Length: 122 amino acids
Theoretical weight: 13.47 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P32774 (Residues: 1-122; Coverage: 100%)
Gene names: TOA2, YKL058W
Sequence domains:
Transcription initiation factor IIF subunit alpha Chain: f
Molecule details ›
Chain: f
Length: 735 amino acids
Theoretical weight: 82.32 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41895 (Residues: 1-735; Coverage: 100%)
Gene names: G7526, SSU71, TFG1, YGR186W
Sequence domains: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
Transcription initiation factor IIF subunit beta Chain: g
Molecule details ›
Chain: g
Length: 400 amino acids
Theoretical weight: 46.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41896 (Residues: 1-400; Coverage: 100%)
Gene names: TFG2, YGR005C
Sequence domains:
Transcription initiation factor IIE subunit alpha Chain: h
Molecule details ›
Chain: h
Length: 482 amino acids
Theoretical weight: 54.8 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P36100 (Residues: 1-482; Coverage: 100%)
Gene names: TFA1, YKL028W
Sequence domains: TFIIE alpha subunit
Transcription initiation factor IIE subunit beta Chain: i
Molecule details ›
Chain: i
Length: 328 amino acids
Theoretical weight: 37.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P36145 (Residues: 1-328; Coverage: 100%)
Gene names: TFA2, YKR062W
Sequence domains:
TATA-box-binding protein Chain: j
Molecule details ›
Chain: j
Length: 240 amino acids
Theoretical weight: 27.04 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P13393 (Residues: 1-240; Coverage: 100%)
Gene names: BTF1, SPT15, TBP1, YER148W
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
DNA-directed RNA polymerase II subunit RPB1 Chain: k
Molecule details ›
Chain: k
Length: 25 amino acids
Theoretical weight: 2.61 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
UniProt:
  • Canonical: P04050 (Residues: 1666-1690; Coverage: 1%)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
Sequence domains: RNA polymerase Rpb1 C-terminal repeat
Transcription initiation factor TFIID subunit 14 Chain: n
Molecule details ›
Chain: n
Length: 244 amino acids
Theoretical weight: 27.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P35189 (Residues: 1-244; Coverage: 100%)
Gene names: ANC1, CST10, SWP29, TAF14, TAF30, TFG3, YPL129W
Sequence domains:
108bp HIS4 Promoter Non-template Strand (-92/+16) Chain: l
Molecule details ›
Chain: l
Length: 108 nucleotides
Theoretical weight: 33.32 KDa
108bp HIS4 Promoter Template Strand (+16/-92) Chain: m
Molecule details ›
Chain: m
Length: 108 nucleotides
Theoretical weight: 33.31 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 15.3Å
Relevant EMDB volumes: EMD-8305
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

42 review citations

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

5 mentions without citation

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