› 5oik

Electron Microscopy
3.7Å resolution

Structure of an RNA polymerase II-DSIF transcription elongation complex

Released:
DOI: 10.2210/pdb5oik/pdb
PDB entry 5oik coloured by chain, front view.
PDB entry 5oik coloured by chain, side view.
PDB entry 5oik coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Bernecky C, Plitzko JM, Cramer P
Nat Struct Mol Biol 24 809-815 (2017)
PMID: 28892040
Related structures: EMD-3817

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107717 (preferred)
Entry contents:
14 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (17 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.44 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: G3MZY8 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: A5PJW8 (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: 31.47 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q3T0Q3 (Residues: 1-275; Coverage: 100%)
Gene name: POLR2C
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.35 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q1JQ91 (Residues: 1-142; Coverage: 100%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
Structure domains: Growth Hormone; Chain: A;
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.51 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2T9T3 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Sequence domains:
Structure 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: Bos taurus
UniProt:
  • Canonical: Q32PE0 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q5E9B8 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
Sequence domains:
Structure 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: Bos taurus
UniProt:
  • Canonical: F2Z4H3 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Sequence domains: RNA polymerase Rpb8
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 14.51 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q32P73 (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: Bos taurus
UniProt:
  • Canonical: Q32P78 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
Structure domains: Homeodomain-like
DNA-directed RNA polymerase II subunit RPB11 Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q32P79 (Residues: 1-117; Coverage: 100%)
Gene name: POLR2J
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
Structure domains: RNA polymerase, RBP11-like subunit
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: Bos taurus
UniProt:
  • Canonical: Q3ZBC0 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
Transcription elongation factor SPT4 Chain: Y
Molecule details ›
Chain: Y
Length: 117 amino acids
Theoretical weight: 13.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63272 (Residues: 1-117; Coverage: 100%)
Gene names: SPT4H, SUPT4H, SUPT4H1
Sequence domains: Spt4/RpoE2 zinc finger
Structure domains: Herpes Virus-1
Transcription elongation factor SPT5 Chain: Z
Molecule details ›
Chain: Z
Length: 1087 amino acids
Theoretical weight: 121.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O00267 (Residues: 1-1087; Coverage: 100%)
Gene names: SPT5, SPT5H, SUPT5H
Sequence domains:
DNA (43-MER) Chain: N
Molecule details ›
Chain: N
Length: 43 nucleotides
Theoretical weight: 13.3 KDa
DNA (43-MER) Chain: T
Molecule details ›
Chain: T
Length: 43 nucleotides
Theoretical weight: 13.18 KDa
RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 50 nucleotides
Theoretical weight: 16.08 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-3817
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

21 review citations

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

16 mentions without citation

Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans.
Dollinger et al. (2021)
15 more