› 8wan

Electron Microscopy
6.07Å resolution

Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS.

Released:
DOI: 10.2210/pdb8wan/pdb
PDB entry 8wan coloured by chain, front view.
PDB entry 8wan coloured by chain, side view.
PDB entry 8wan coloured by chain, top view.
Source organisms:
Primary publication:
Structural visualization of transcription initiation in action.
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science 382 eadi5120 (2023)
PMID: 38127763
Related structures: EMD-37398

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 51-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236179 (preferred)
Entry contents:
42 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (45 distinct):
CDK-activating kinase assembly factor MAT1 Chain: 0
Molecule details ›
Chain: 0
Length: 309 amino acids
Theoretical weight: 35.87 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P51948 (Residues: 1-309; Coverage: 100%)
Gene names: CAP35, MAT1, MNAT1, RNF66
Sequence domains:
General transcription factor IIH subunit 1 Chain: 1
Molecule details ›
Chain: 1
Length: 548 amino acids
Theoretical weight: 62.12 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P32780 (Residues: 1-548; Coverage: 100%)
Gene names: BTF2, GTF2H1
Sequence domains:
General transcription factor IIH subunit 2 Chain: 2
Molecule details ›
Chain: 2
Length: 395 amino acids
Theoretical weight: 44.48 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13888 (Residues: 1-395; Coverage: 100%)
Gene names: BTF2P44, GTF2H2
Sequence domains:
General transcription factor IIH subunit 3 Chain: 3
Molecule details ›
Chain: 3
Length: 308 amino acids
Theoretical weight: 34.42 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13889 (Residues: 1-308; Coverage: 100%)
Gene name: GTF2H3
Sequence domains: Transcription factor Tfb4
General transcription factor IIH subunit 4 Chain: 4
Molecule details ›
Chain: 4
Length: 462 amino acids
Theoretical weight: 52.25 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q92759 (Residues: 1-462; Coverage: 100%)
Gene name: GTF2H4
Sequence domains:
General transcription factor IIH subunit 5 Chain: 5
Molecule details ›
Chain: 5
Length: 71 amino acids
Theoretical weight: 8.06 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6ZYL4 (Residues: 1-71; Coverage: 100%)
Gene names: C6orf175, GTF2H5, TTDA
Sequence domains: Transcription factor TFIIH complex subunit Tfb5
General transcription and DNA repair factor IIH helicase/translocase subunit XPB Chain: 6
Molecule details ›
Chain: 6
Length: 782 amino acids
Theoretical weight: 89.4 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P19447 (Residues: 1-782; Coverage: 100%)
Gene names: ERCC3, XPB, XPBC
Sequence domains:
General transcription and DNA repair factor IIH helicase subunit XPD Chain: 7
Molecule details ›
Chain: 7
Length: 760 amino acids
Theoretical weight: 87.02 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P18074 (Residues: 1-760; Coverage: 100%)
Gene names: ERCC2, XPD, XPDC
Sequence domains:
Alpha-amanitin Chain: N
Molecule details ›
Chain: N
Length: 8 amino acids
Theoretical weight: 939 Da
Source organism: Amanita phalloides
UniProt:
  • Canonical: P85421 (Residues: 1-8; Coverage: 35%)
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:
General transcription factor IIE subunit 1 Chain: U
Molecule details ›
Chain: U
Length: 439 amino acids
Theoretical weight: 49.52 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P29083 (Residues: 1-439; Coverage: 100%)
Gene names: GTF2E1, TF2E1
Sequence domains:
Transcription initiation factor IIE subunit beta Chain: V
Molecule details ›
Chain: V
Length: 291 amino acids
Theoretical weight: 33.11 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P29084 (Residues: 1-291; Coverage: 100%)
Gene names: GTF2E2, TF2E2
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: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1DPV6 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
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: A0A4X1TVZ5 (Residues: 78-1251; Coverage: 94%)
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: A0A481BYI6 (Residues: 1-142; Coverage: 100%)
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: A0A4X1VTX4 (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 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-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: A0A493TD97 (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
non-template DNA Chain: X
Molecule details ›
Chain: X
Length: 99 nucleotides
Theoretical weight: 30.61 KDa
template DNA Chain: Y
Molecule details ›
Chain: Y
Length: 99 nucleotides
Theoretical weight: 30.48 KDa
RNA Chain: Z
Molecule details ›
Chain: Z
Length: 4 nucleotides
Theoretical weight: 1.46 KDa

Ligands and Environments

4 bound ligands:
Ligand ZN 17 x ZN
Ligand SF4 1 x SF4
Ligand MG 1 x MG
Ligand W0F 1 x W0F
5 modified residues:
Ligand ILX 1 x ILX
Ligand TRX 1 x TRX
Ligand CSX 1 x CSX
Ligand HYP 1 x HYP
Ligand G2L 1 x G2L

Experiments and Validation Details

Entry percentile scores
Resolution: 6.07Å
Relevant EMDB volumes: EMD-37398
Expression system: Homo sapiens

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