› 5iy8

Electron Microscopy
7.9Å resolution

Human holo-PIC in the initial transcribing state

Released:
DOI: 10.2210/pdb5iy8/pdb
PDB entry 5iy8 coloured by chain, front view.
PDB entry 5iy8 coloured by chain, side view.
PDB entry 5iy8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Near-atomic resolution visualization of human transcription promoter opening.
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E
Nature 533 359-65 (2016)
PMID: 27193682
Related structures: EMD-8133

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 29-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118817 (preferred)
Entry contents:
27 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (29 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P24928 (Residues: 1-1970; Coverage: 100%)
Gene names: POLR2, POLR2A
Sequence domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P30876 (Residues: 1-1174; Coverage: 100%)
Gene name: POLR2B
Sequence domains:
DNA-directed RNA polymerase II subunit RPB3 Chain: C
Molecule details ›
Chain: C
Length: 275 amino acids
Theoretical weight: 31.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P19387 (Residues: 1-275; Coverage: 100%)
Gene names: A-152E5.7, POLR2C
Sequence domains:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15514 (Residues: 1-142; Coverage: 100%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P19388 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61218 (Residues: 1-127; Coverage: 100%)
Gene names: POLR2F, POLRF
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62487 (Residues: 1-172; Coverage: 100%)
Gene names: POLR2G, RPB7
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 150 amino acids
Theoretical weight: 17.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P52434 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P36954 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62875 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase II subunit RPB11-a Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P52435 (Residues: 1-117; Coverage: 100%)
Gene names: POLR2J, POLR2J1
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P53803 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription initiation factor IIB Chain: M
Molecule details ›
Chain: M
Length: 316 amino acids
Theoretical weight: 34.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00403 (Residues: 1-316; Coverage: 100%)
Gene names: GTF2B, TF2B, TFIIB
Sequence domains:
Transcription initiation factor IIA subunit 1 Chain: N
Molecule details ›
Chain: N
Length: 376 amino acids
Theoretical weight: 41.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P52655 (Residues: 1-376; Coverage: 100%)
Gene names: GTF2A1, TF2A1
Sequence domains: Transcription factor IIA, alpha/beta subunit
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: Escherichia coli
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: Escherichia coli
UniProt:
  • Canonical: P20226 (Residues: 1-339; Coverage: 100%)
Gene names: GTF2D1, TBP, TF2D, TFIID
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
General transcription factor IIE subunit 1 Chain: Q
Molecule details ›
Chain: Q
Length: 439 amino acids
Theoretical weight: 49.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P29083 (Residues: 1-439; Coverage: 100%)
Gene names: GTF2E1, TF2E1
Sequence domains:
Transcription initiation factor IIE subunit beta Chain: R
Molecule details ›
Chain: R
Length: 291 amino acids
Theoretical weight: 33.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P29084 (Residues: 1-291; Coverage: 100%)
Gene names: GTF2E2, TF2E2
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: Escherichia coli
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: Escherichia coli
UniProt:
  • Canonical: P13984 (Residues: 1-249; Coverage: 100%)
Gene names: GTF2F2, RAP30
Sequence domains:
Transcription elongation factor A protein 1 Chain: U
Molecule details ›
Chain: U
Length: 301 amino acids
Theoretical weight: 34.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23193 (Residues: 1-301; Coverage: 100%)
Gene names: GTF2S, TCEA1, TFIIS
Sequence domains:
General transcription and DNA repair factor IIH helicase/translocase subunit XPB Chain: V
Molecule details ›
Chain: V
Length: 782 amino acids
Theoretical weight: 89.4 KDa
Source organism: 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: W
Molecule details ›
Chain: W
Length: 760 amino acids
Theoretical weight: 87.02 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P18074 (Residues: 1-760; Coverage: 100%)
Gene names: ERCC2, XPD, XPDC
Sequence domains:
General transcription factor IIH subunit 2 Chain: 0
Molecule details ›
Chain: 0
Length: 395 amino acids
Theoretical weight: 44.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13888 (Residues: 1-395; Coverage: 100%)
Gene names: BTF2P44, GTF2H2
Sequence domains:
General transcription factor IIH subunit 5 Chain: 1
Molecule details ›
Chain: 1
Length: 71 amino acids
Theoretical weight: 8.06 KDa
Source organism: 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 factor IIH subunit 4 Chain: 2
Molecule details ›
Chain: 2
Length: 462 amino acids
Theoretical weight: 52.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92759 (Residues: 1-462; Coverage: 100%)
Gene name: GTF2H4
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
UniProt:
  • Canonical: Q13889 (Residues: 1-308; Coverage: 100%)
Gene name: GTF2H3
Sequence domains: Transcription factor Tfb4
SCP-X Chain: X
Molecule details ›
Chain: X
Length: 83 nucleotides
Theoretical weight: 25.77 KDa
SCP-Y Chain: Y
Molecule details ›
Chain: Y
Length: 83 nucleotides
Theoretical weight: 25.38 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ZN 11 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7.9Å
Relevant EMDB volumes: EMD-8133
Expression system: Escherichia coli

Quick links

Citations

51 review citations

Eukaryotic core promoters and the functional basis of transcription initiation.
Haberle et al. (2018)
50 more

3 mentions without citation

Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation.
Herbert A. (2023)
2 more