› 6ted

Electron Microscopy
3.1Å resolution

Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1

Released:
DOI: 10.2210/pdb6ted/pdb
PDB entry 6ted coloured by chain, front view.
PDB entry 6ted coloured by chain, side view.
PDB entry 6ted coloured by chain, top view.
Source organisms:
Primary publication:
Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation.
Vos SM, Farnung L, Linden A, Urlaub H, Cramer P
Nat Struct Mol Biol 27 668-677 (2020)
PMID: 32541898
Related structures: EMD-10480

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 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-288629 (preferred)
Entry contents:
21 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (24 distinct):
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 1984 amino acids
Theoretical weight: 219.05 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A7M4DUC2 (Residues: 1-1984; Coverage: 100%)
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1251 amino acids
Theoretical weight: 142.43 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 50-1300; Coverage: 96%)
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
RNA polymerase II subunit G 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 RBP11-like dimerisation domain-containing protein Chain: K
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Transcription elongation factor SPT6 Chain: M
RNA polymerase-associated protein CTR9 homolog Chain: Q
RNA polymerase-associated protein RTF1 homolog Chain: R
RNA polymerase-associated protein LEO1 Chain: U
RNA polymerase II-associated factor 1 homolog Chain: V
Superkiller complex protein 8 Chain: W
Parafibromin Chain: X
Transcription elongation factor SPT4 Chain: Y
Transcription elongation factor SPT5 Chain: Z
DNA (37-MER) Chain: N
Template DNA Chain: T
RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3') Chain: P

Ligands and Environments

2 bound ligands:
Ligand ZN 9 x ZN
Ligand MG 1 x MG
2 modified residues:
Ligand TPO 2 x TPO
Ligand SEP 1 x SEP

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.1Å
Relevant EMDB volumes: EMD-10480
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

13 review citations

Causes and consequences of RNA polymerase II stalling during transcript elongation.
Noe Gonzalez et al. (2021)
12 more

11 mentions without citation

The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin.
Francette et al. (2021)
10 more