› 4v1o

Electron Microscopy
9.7Å resolution

Architecture of the RNA polymerase II-Mediator core transcription initiation complex

Released:
DOI: 10.2210/pdb4v1o/pdb
PDB entry 4v1o coloured by chain, front view.
PDB entry 4v1o coloured by chain, side view.
PDB entry 4v1o coloured by chain, top view.
Source organisms:
Primary publication:
Architecture of the RNA polymerase II-Mediator core initiation complex.
Plaschka C, Larivière L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P
Nature 518 376-80 (2015)
PMID: 25652824
Related structures: EMD-2786

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 26-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101383 (preferred)
Entry contents:
23 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (26 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
Expression system: Escherichia coli
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription initiation factor IIB Chain: M
Molecule details ›
Chain: M
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:
TATA-box-binding protein Chain: O
Molecule details ›
Chain: O
Length: 181 amino acids
Theoretical weight: 20.25 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P13393 (Residues: 61-240; Coverage: 75%)
Gene names: BTF1, SPT15, TBP1, YER148W
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
Transcription initiation factor IIF subunit alpha Chain: Q
Molecule details ›
Chain: Q
Length: 734 amino acids
Theoretical weight: 82.37 KDa
Source organism: Saccharomyces mikatae
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0H2UKZ8 (Residues: 1-734; Coverage: 100%)
Sequence domains: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
Transcription initiation factor IIF subunit beta Chain: R
Molecule details ›
Chain: R
Length: 331 amino acids
Theoretical weight: 37.92 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P41896 (Residues: 1-400; Coverage: 83%)
Gene names: TFG2, YGR005C
Sequence domains:
Mediator of RNA polymerase II transcription subunit 6 Chain: S
Molecule details ›
Chain: S
Length: 295 amino acids
Theoretical weight: 32.84 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
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: U
Molecule details ›
Chain: U
Length: 222 amino acids
Theoretical weight: 25.17 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P38304 (Residues: 2-223; 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: V
Molecule details ›
Chain: V
Length: 115 amino acids
Theoretical weight: 13.32 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
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: W
Molecule details ›
Chain: W
Length: 687 amino acids
Theoretical weight: 78.51 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P32569 (Residues: 2-687; Coverage: 100%)
Gene names: MED17, SRB4, YER022W
Sequence domains: Subunit 17 of Mediator complex
Mediator of RNA polymerase II transcription subunit 18 Chain: X
Molecule details ›
Chain: X
Length: 307 amino acids
Theoretical weight: 34.32 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
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: Y
Molecule details ›
Chain: Y
Length: 209 amino acids
Theoretical weight: 22.79 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P34162 (Residues: 2-210; 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: Z
Molecule details ›
Chain: Z
Length: 120 amino acids
Theoretical weight: 13.74 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P32570 (Residues: 2-121; Coverage: 99%)
Gene names: MED22, SRB6, YBR1721, YBR253W
Sequence domains: Surfeit locus protein 5 subunit 22 of Mediator complex
NONTEMPLATE DNA Chain: N
Molecule details ›
Chain: N
Length: 50 nucleotides
Theoretical weight: 15.45 KDa
TEMPLATE DNA Chain: T
Molecule details ›
Chain: T
Length: 58 nucleotides
Theoretical weight: 17.81 KDa
RNA Chain: P
Molecule details ›
Chain: P
Length: 6 nucleotides
Theoretical weight: 1.86 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 9 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 9.7Å
Relevant EMDB volumes: EMD-2786
Expression system: Escherichia coli

Quick links

Citations

57 review citations

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

5 mentions without citation

Zooming in on Transcription Preinitiation.
Gupta et al. (2016)
4 more