› 7eg7

Electron Microscopy
6.2Å resolution

TFIID-based core PIC on SCP promoter

Released:
DOI: 10.2210/pdb7eg7/pdb
PDB entry 7eg7 coloured by chain, front view.
PDB entry 7eg7 coloured by chain, side view.
PDB entry 7eg7 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into preinitiation complex assembly on core promoters.
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science 372 (2021)
PMID: 33795473
Related structures: EMD-31107

Function and Biology Details

Reactions catalysed: 
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
ATP + a protein = ADP + a phosphoprotein
ATP + H(2)O = ADP + phosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 39-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236727 (preferred)
Entry contents:
31 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (33 distinct):
Transcription initiation factor TFIID subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 1872 amino acids
Theoretical weight: 212.96 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P21675 (Residues: 1-1893; Coverage: 99%)
Gene names: BA2R, CCG1, CCGS, TAF1, TAF2A
Sequence domains:
Transcription initiation factor TFIID subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 1199 amino acids
Theoretical weight: 137.16 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6P1X5 (Residues: 1-1199; Coverage: 100%)
Gene names: CIF150, TAF2, TAF2B
Transcription initiation factor TFIID subunit 4 Chains: D, d
Molecule details ›
Chains: D, d
Length: 1085 amino acids
Theoretical weight: 110.22 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O00268 (Residues: 1-1085; Coverage: 100%)
Gene names: TAF2C, TAF2C1, TAF4, TAF4A, TAFII130, TAFII135
Sequence domains:
Transcription initiation factor TFIID subunit 5 Chains: E, e
Molecule details ›
Chains: E, e
Length: 800 amino acids
Theoretical weight: 86.93 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15542 (Residues: 1-800; Coverage: 100%)
Gene names: TAF2D, TAF5
Sequence domains:
Transcription initiation factor TFIID subunit 6 Chains: F, f
Molecule details ›
Chains: F, f
Length: 677 amino acids
Theoretical weight: 72.75 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P49848 (Residues: 1-677; Coverage: 100%)
Gene names: TAF2E, TAF6, TAFII70
Sequence domains:
Transcription initiation factor TFIID subunit 7 Chain: G
Molecule details ›
Chain: G
Length: 349 amino acids
Theoretical weight: 40.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15545 (Residues: 1-349; Coverage: 100%)
Gene names: TAF2F, TAF7, TAFII55
Sequence domains: TAFII55 protein conserved region
Transcription initiation factor TFIID subunit 8 Chain: H
Molecule details ›
Chain: H
Length: 310 amino acids
Theoretical weight: 34.3 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q7Z7C8 (Residues: 1-310; Coverage: 100%)
Gene names: TAF8, TAFII43, TBN
Sequence domains:
Transcription initiation factor TFIID subunit 9 Chains: I, i
Molecule details ›
Chains: I, i
Length: 264 amino acids
Theoretical weight: 29.01 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q16594 (Residues: 1-264; Coverage: 100%)
Gene names: TAF2G, TAF9, TAFII31
Sequence domains: Transcription initiation factor IID, 31kD subunit
Transcription initiation factor TFIID subunit 10 Chains: J, j
Molecule details ›
Chains: J, j
Length: 218 amino acids
Theoretical weight: 21.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q12962 (Residues: 1-218; Coverage: 100%)
Gene names: TAF10, TAF2A, TAF2H, TAFII30
Sequence domains: Transcription initiation factor TFIID 23-30kDa subunit
Transcription initiation factor TFIID subunit 12 Chains: L, l
Molecule details ›
Chains: L, l
Length: 161 amino acids
Theoretical weight: 17.95 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q16514 (Residues: 1-161; Coverage: 100%)
Gene names: TAF12, TAF15, TAF2J, TAFII20
Sequence domains: Transcription initiation factor TFIID subunit A
Transcription initiation factor IIA subunit 2 Chain: O
Molecule details ›
Chain: O
Length: 109 amino acids
Theoretical weight: 12.47 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P52657 (Residues: 1-109; Coverage: 100%)
Gene names: GTF2A2, TF2A2
Sequence domains:
TATA-box-binding protein Chain: P
Molecule details ›
Chain: P
Length: 339 amino acids
Theoretical weight: 37.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P20226 (Residues: 1-339; Coverage: 100%)
Gene names: GTF2D1, TBP, TF2D, TFIID
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
Transcription initiation factor IIA subunit 1 Chain: Q
Molecule details ›
Chain: Q
Length: 376 amino acids
Theoretical weight: 41.54 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P52655 (Residues: 1-376; Coverage: 100%)
Gene names: GTF2A1, TF2A1
Sequence domains: Transcription factor IIA, alpha/beta subunit
Transcription initiation factor IIB Chain: R
Molecule details ›
Chain: R
Length: 316 amino acids
Theoretical weight: 34.88 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q00403 (Residues: 1-316; Coverage: 100%)
Gene names: GTF2B, TF2B, TFIIB
Sequence domains:
General transcription factor IIF subunit 1 Chain: S
Molecule details ›
Chain: S
Length: 517 amino acids
Theoretical weight: 58.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P35269 (Residues: 1-517; Coverage: 100%)
Gene names: GTF2F1, RAP74
Sequence domains: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
General transcription factor IIF subunit 2 Chain: T
Molecule details ›
Chain: T
Length: 249 amino acids
Theoretical weight: 28.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P13984 (Residues: 1-249; Coverage: 100%)
Gene names: GTF2F2, RAP30
Sequence domains:
Transcription initiation factor TFIID subunit 3 Chain: c
Molecule details ›
Chain: c
Length: 929 amino acids
Theoretical weight: 103.77 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q5VWG9 (Residues: 1-929; Coverage: 100%)
Gene name: TAF3
Sequence domains:
Transcription initiation factor TFIID subunit 11 Chain: k
Molecule details ›
Chain: k
Length: 211 amino acids
Theoretical weight: 23.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15544 (Residues: 1-211; Coverage: 100%)
Gene names: PRO2134, TAF11, TAF2I
Sequence domains: hTAFII28-like protein conserved region
Transcription initiation factor TFIID subunit 13 Chain: m
Molecule details ›
Chain: m
Length: 124 amino acids
Theoretical weight: 14.31 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15543 (Residues: 1-124; Coverage: 100%)
Gene names: TAF13, TAF2K, TAFII18
Sequence domains: Transcription initiation factor IID, 18kD subunit
DNA-directed RNA polymerase subunit Chain: o
Molecule details ›
Chain: o
Length: 1970 amino acids
Theoretical weight: 217.42 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A7M4DUC2 (Residues: 1-1984; Coverage: 99%)
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: p
Molecule details ›
Chain: p
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 127-1300; Coverage: 90%)
Gene name: POLR2B
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chain: q
Molecule details ›
Chain: q
Length: 275 amino acids
Theoretical weight: 31.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCH3 (Residues: 1-275; Coverage: 100%)
Gene name: POLR2C
Sequence domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: r
Molecule details ›
Chain: r
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 43-184; Coverage: 77%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerase II subunit E Chain: s
Molecule details ›
Chain: s
Length: 210 amino acids
Theoretical weight: 24.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LSI7 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: t
Molecule details ›
Chain: t
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: v
Molecule details ›
Chain: v
Length: 150 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCB2 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: w
Molecule details ›
Chain: w
Length: 125 amino acids
Theoretical weight: 14.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P60899 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: x
Molecule details ›
Chain: x
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VYD0 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chain: y
Molecule details ›
Chain: y
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RKE4 (Residues: 1-117; Coverage: 100%)
Gene name: POLR2J
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: z
Molecule details ›
Chain: z
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TRS6 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
DNA-directed RNA polymerase subunit Chain: u
Molecule details ›
Chain: u
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VKG7 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
Sequence domains:
DNA (79-MER) Chain: X
Molecule details ›
Chain: X
Length: 79 nucleotides
Theoretical weight: 24.51 KDa
DNA (79-MER) Chain: Y
Molecule details ›
Chain: Y
Length: 79 nucleotides
Theoretical weight: 24.22 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: 6.2Å
Relevant EMDB volumes: EMD-31107
Expression system: Homo sapiens

Quick links

Citations

12 review citations

The Mediator complex as a master regulator of transcription by RNA polymerase II.
Richter et al. (2022)
11 more

2 mentions without citation

Assembly of RNA polymerase II transcription initiation complexes.
Farnung et al. (2022)
1 more