› 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
DNA-directed RNA polymerase II subunit RPB4 Chain: D
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
DNA-directed RNA polymerase II subunit RPB7 Chain: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
DNA-directed RNA polymerase II subunit RPB9 Chain: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
DNA-directed RNA polymerase II subunit RPB11-a Chain: K
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Transcription initiation factor IIB Chain: M
Transcription initiation factor IIA subunit 1 Chain: N
Transcription initiation factor IIA subunit 2 Chain: O
TATA-box-binding protein Chain: P
General transcription factor IIE subunit 1 Chain: Q
Transcription initiation factor IIE subunit beta Chain: R
General transcription factor IIF subunit 1 Chain: S
General transcription factor IIF subunit 2 Chain: T
Transcription elongation factor A protein 1 Chain: U
General transcription and DNA repair factor IIH helicase/translocase subunit XPB Chain: V
General transcription and DNA repair factor IIH helicase subunit XPD Chain: W
General transcription factor IIH subunit 2 Chain: 0
General transcription factor IIH subunit 5 Chain: 1
General transcription factor IIH subunit 4 Chain: 2
General transcription factor IIH subunit 3 Chain: 3
SCP-X Chain: X
SCP-Y Chain: Y

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
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