› 7uio

Electron Microscopy
3.3Å resolution

Mediator-PIC Early (Composite Model)

Released:
DOI: 10.2210/pdb7uio/pdb
PDB entry 7uio coloured by chain, front view.
PDB entry 7uio coloured by chain, side view.
PDB entry 7uio coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural basis of a transcription pre-initiation complex on a divergent promoter.
Gorbea Colón JJ, Palao L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K
Mol Cell (2023)
PMID: 36731470
Related structures: EMD-26551

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 80-mer (preferred)
PDBe Complex ID:
PDB-CPX-122190 (preferred)
Entry contents:
39 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (41 distinct):
Mediator of RNA polymerase II transcription subunit 15 Chains: Ao, Bo
Molecule details ›
Chains: Ao, Bo
Length: 1081 amino acids
Theoretical weight: 120.43 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P19659 (Residues: 1-1081; Coverage: 100%)
Gene names: ABE1, GAL11, MED15, RAR3, SDS4, SPT13, YOL051W
Sequence domains:
Mediator of RNA polymerase II transcription subunit 2 Chains: Ab, Bb
Molecule details ›
Chains: Ab, Bb
Length: 431 amino acids
Theoretical weight: 47.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12124 (Residues: 1-431; Coverage: 100%)
Gene names: D2930, MED2, YDL005C
Sequence domains: Mediator complex subunit 2
Mediator of RNA polymerase II transcription subunit 3 Chains: Ac, Bc
Molecule details ›
Chains: Ac, Bc
Length: 397 amino acids
Theoretical weight: 43.12 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40356 (Residues: 1-397; Coverage: 100%)
Gene names: HRS1, MED3, PGD1, YGL025C
Sequence domains: Mediator complex subunit 3 fungal
Mediator of RNA polymerase II transcription subunit 14 Chains: An, Bn
Molecule details ›
Chains: An, Bn
Length: 1082 amino acids
Theoretical weight: 123.5 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P19263 (Residues: 1-1082; Coverage: 100%)
Gene names: MED14, RGR1, YLR071C
Sequence domains: Mediator complex subunit MED14
Mediator of RNA polymerase II transcription subunit 5 Chains: Ae, Be
Molecule details ›
Chains: Ae, Be
Length: 1132 amino acids
Theoretical weight: 128.92 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53114 (Residues: 1-1132; Coverage: 100%)
Gene names: G1876, MED5, NUT1, YGL151W
Sequence domains: Mediator complex subunit Med5
Mediator of RNA polymerase II transcription subunit 16 Chains: Ap, Bp
Molecule details ›
Chains: Ap, Bp
Length: 974 amino acids
Theoretical weight: 111.42 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32259 (Residues: 1-974; Coverage: 100%)
Gene names: BEL2, GAL22, MED16, N1135, RYE1, SDI3, SIN4, SSF5, SSN4, TSF3, YNL236W
Sequence domains:
Regulatory protein GAL4 Chains: GA, GB
Molecule details ›
Chains: GA, GB
Length: 147 amino acids
Theoretical weight: 16.9 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P04386 (Residues: 1-147; Coverage: 17%)
Gene names: GAL4, YPL248C
Sequence domains:
Mediator of RNA polymerase II transcription subunit 20 Chains: At, Bt
Molecule details ›
Chains: At, Bt
Length: 210 amino acids
Theoretical weight: 22.92 KDa
Source organism: Saccharomyces cerevisiae S288C
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 7 Chains: Ag, Bg
Molecule details ›
Chains: Ag, Bg
Length: 222 amino acids
Theoretical weight: 25.62 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08278 (Residues: 1-222; Coverage: 100%)
Gene names: MED7, YOL135C
Sequence domains: MED7 protein
Mediator of RNA polymerase II transcription subunit 8 Chains: Ah, Bh
Molecule details ›
Chains: Ah, Bh
Length: 223 amino acids
Theoretical weight: 25.3 KDa
Source organism: Saccharomyces cerevisiae S288C
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 9 Chains: Ai, Bi
Molecule details ›
Chains: Ai, Bi
Length: 149 amino acids
Theoretical weight: 17.4 KDa
Source organism: Saccharomyces cerevisiae S288C
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 10 Chains: Aj, Bj
Molecule details ›
Chains: Aj, Bj
Length: 157 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06213 (Residues: 1-157; Coverage: 100%)
Gene names: MED10, NUT2, P9325.2, YPR168W
Sequence domains: Transcription factor subunit Med10 of Mediator complex
Mediator of RNA polymerase II transcription subunit 11 Chains: Ak, Bk
Molecule details ›
Chains: Ak, Bk
Length: 115 amino acids
Theoretical weight: 13.32 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: Aq, Bq
Molecule details ›
Chains: Aq, Bq
Length: 687 amino acids
Theoretical weight: 78.58 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: Ar, Br
Molecule details ›
Chains: Ar, Br
Length: 307 amino acids
Theoretical weight: 34.32 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32585 (Residues: 1-307; Coverage: 100%)
Gene names: MED18, SRB5, YGR104C
Sequence domains: Med18 protein
Mediator of RNA polymerase II transcription subunit 19 Chains: As, Bs
Molecule details ›
Chains: As, Bs
Length: 220 amino acids
Theoretical weight: 24.89 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25046 (Residues: 1-220; Coverage: 100%)
Gene names: MED19, NUT3, ROX3, SSN7, YBL0837, YBL093C
Sequence domains: Rox3 mediator complex subunit
Mediator of RNA polymerase II transcription subunit 21 Chains: Au, Bu
Molecule details ›
Chains: Au, Bu
Length: 140 amino acids
Theoretical weight: 16.09 KDa
Source organism: Saccharomyces cerevisiae S288C
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 22 Chains: Av, Bv
Molecule details ›
Chains: Av, Bv
Length: 120 amino acids
Theoretical weight: 13.77 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32570 (Residues: 1-120; Coverage: 99%)
Gene names: MED22, SRB6, YBR1721, YBR253W
Sequence domains: Surfeit locus protein 5 subunit 22 of Mediator complex
Mediator of RNA polymerase II transcription subunit 31 Chains: Aw, Bw
Molecule details ›
Chains: Aw, Bw
Length: 127 amino acids
Theoretical weight: 14.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38633 (Residues: 1-127; Coverage: 100%)
Gene names: G2864, MED31, SOH1, YGL127C
Sequence domains: SOH1
DNA-directed RNA polymerase II subunit RPB1 Chains: Az, Bz
Molecule details ›
Chains: Az, Bz
Length: 25 amino acids
Theoretical weight: 2.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04050 (Residues: 1666-1690; Coverage: 1%)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
Sequence domains: RNA polymerase Rpb1 C-terminal repeat
DNA-directed RNA polymerase II subunit RPB1 Chains: AA, BA
Molecule details ›
Chains: AA, BA
Length: 1453 amino acids
Theoretical weight: 162.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04050 (Residues: 1-1453; Coverage: 84%)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
Sequence domains:
DNA-directed RNA polymerase II subunit RPB2 Chains: AB, BB
Molecule details ›
Chains: AB, BB
Length: 1224 amino acids
Theoretical weight: 138.94 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P08518 (Residues: 1-1224; Coverage: 100%)
Gene names: RPB150, RPB2, RPO22, YOR151C
Sequence domains:
DNA-directed RNA polymerase II subunit RPB3 Chains: AC, BC
Molecule details ›
Chains: AC, BC
Length: 318 amino acids
Theoretical weight: 35.33 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P16370 (Residues: 1-318; Coverage: 100%)
Gene names: RPB3, YIL021W
Sequence domains:
DNA-directed RNA polymerase II subunit RPB4 Chains: AD, BD
Molecule details ›
Chains: AD, BD
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: AE, BE
Molecule details ›
Chains: AE, BE
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: AF, BF
Molecule details ›
Chains: AF, BF
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: AG, BG
Molecule details ›
Chains: AG, BG
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: AH, BH
Molecule details ›
Chains: AH, BH
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: AI, BI
Molecule details ›
Chains: AI, BI
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P27999 (Residues: 1-122; Coverage: 100%)
Gene names: RPB9, YGL070C
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chains: AJ, BJ
Molecule details ›
Chains: AJ, BJ
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: AK, BK
Molecule details ›
Chains: AK, BK
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Gene names: RPB11, YOL005C
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chains: AL, BL
Molecule details ›
Chains: AL, BL
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: AM, BM
Molecule details ›
Chains: AM, BM
Length: 345 amino acids
Theoretical weight: 38.26 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P29055 (Residues: 1-345; Coverage: 100%)
Gene names: P9513.4, SUA7, YPR086W
Sequence domains:
Transcription initiation factor IIF subunit alpha Chains: AP, BP
Molecule details ›
Chains: AP, BP
Length: 735 amino acids
Theoretical weight: 82.32 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chains: AQ, BQ
Molecule details ›
Chains: AQ, BQ
Length: 400 amino acids
Theoretical weight: 46.68 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P41896 (Residues: 1-400; Coverage: 100%)
Gene names: TFG2, YGR005C
Sequence domains:
Transcription elongation factor S-II Chains: AS, BS
Molecule details ›
Chains: AS, BS
Length: 309 amino acids
Theoretical weight: 34.9 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P07273 (Residues: 1-309; Coverage: 100%)
Gene names: DST1, PPR2, YGL043W
Sequence domains:
Mediator of RNA polymerase II transcription subunit 1 Chains: Aa, Ba
Molecule details ›
Chains: Aa, Ba
Length: 566 amino acids
Theoretical weight: 64.31 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12321 (Residues: 1-566; Coverage: 100%)
Gene names: MED1, YP9499.25, YPR063W, YPR070W
Sequence domains: Mediator of RNA polymerase II transcription subunit 1
Mediator of RNA polymerase II transcription subunit 4 Chains: Ad, Bd
Molecule details ›
Chains: Ad, Bd
Length: 284 amino acids
Theoretical weight: 32.24 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6 Chains: Af, Bf
Molecule details ›
Chains: Af, Bf
Length: 295 amino acids
Theoretical weight: 32.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38782 (Residues: 1-295; Coverage: 100%)
Gene names: MED6, MTR32, YHR058C
Sequence domains: MED6 mediator sub complex component
DNA (38-MER) Chain: A
Molecule details ›
Chain: A
Length: 38 nucleotides
Theoretical weight: 11.67 KDa
DNA (37-MER) Chain: B
Molecule details ›
Chain: B
Length: 37 nucleotides
Theoretical weight: 11.42 KDa

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand THR 1 x THR
Ligand ALA 1 x ALA
Ligand ASP 1 x ASP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-26551
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators.
Malik et al. (2023)
2 more

1 mention without citation

Structural basis of a transcription pre-initiation complex on a divergent promoter.
Gorbea Colón et al. (2023)