› 6gmh

Electron Microscopy
3.1Å resolution

Structure of activated transcription complex Pol II-DSIF-PAF-SPT6

Released:
DOI: 10.2210/pdb6gmh/pdb
PDB entry 6gmh coloured by chain, front view.
PDB entry 6gmh coloured by chain, side view.
PDB entry 6gmh coloured by chain, top view.
Source organisms:
Primary publication:
Structure of activated transcription complex Pol II-DSIF-PAF-SPT6.
Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P
Nature 560 607-612 (2018)
PMID: 30135578
Related structures: EMD-0031

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 23-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236762 (preferred)
Entry contents:
20 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (23 distinct):
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.61 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LJR4 (Residues: 1-526, 527-1298, 1299-1968; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 127-1300; Coverage: 90%)
Gene name: POLR2B
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chain: C
Molecule details ›
Chain: C
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:
Structure domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 43-184; Coverage: 77%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
Structure domains: Growth Hormone; Chain: A;
DNA-directed RNA polymerase II subunit E Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LSI7 (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: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
RNA polymerase II subunit G Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
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: Sus scrofa
UniProt:
  • Canonical: I3LCB2 (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: 14.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P60899 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Sequence domains:
RPB10 Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
Structure domains: Homeodomain-like
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chain: K
Molecule details ›
Chain: K
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:
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: Sus scrofa
UniProt:
  • Canonical: A0A4X1TRS6 (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 SPT6 Chain: M
Molecule details ›
Chain: M
Length: 1726 amino acids
Theoretical weight: 198.99 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7KZ85 (Residues: 1-1726; Coverage: 100%)
Gene names: KIAA0162, SPT6H, SUPT6H
Sequence domains:
RNA polymerase-associated protein CTR9 homolog Chain: Q
Molecule details ›
Chain: Q
Length: 1178 amino acids
Theoretical weight: 125.71 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6PD62 (Residues: 301-1173; Coverage: 74%)
Gene names: CTR9, KIAA0155, SH2BP1
Sequence domains:
RNA polymerase-associated protein LEO1 Chain: U
Molecule details ›
Chain: U
Length: 776 amino acids
Theoretical weight: 84.88 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8WVC0 (Residues: 1-666; Coverage: 100%)
Gene names: LEO1, RDL
Sequence domains: Leo1-like protein
RNA polymerase II-associated factor 1 homolog Chain: V
Molecule details ›
Chain: V
Length: 613 amino acids
Theoretical weight: 67.03 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8N7H5 (Residues: 1-531; Coverage: 100%)
Gene names: PAF1, PD2
Sequence domains: Paf1
Superkiller complex protein 8 Chain: W
Molecule details ›
Chain: W
Length: 305 amino acids
Theoretical weight: 33.62 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9GZS3 (Residues: 1-305; Coverage: 100%)
Gene names: SKIC8, WDR61
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
CDC73 Chain: X
Molecule details ›
Chain: X
Length: 16 amino acids
Theoretical weight: 1.38 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
Transcription elongation factor SPT4 Chain: Y
Molecule details ›
Chain: Y
Length: 121 amino acids
Theoretical weight: 13.51 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
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: Trichoplusia ni
UniProt:
  • Canonical: O00267 (Residues: 1-1087; Coverage: 100%)
Gene names: SPT5, SPT5H, SUPT5H
Sequence domains:
Non-template DNA Chain: N
Molecule details ›
Chain: N
Length: 48 nucleotides
Theoretical weight: 14.93 KDa
Template DNA Chain: T
Molecule details ›
Chain: T
Length: 48 nucleotides
Theoretical weight: 14.67 KDa
RNA Chain: P
Molecule details ›
Chain: P
Length: 46 nucleotides
Theoretical weight: 14.84 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-0031
Expression system: Trichoplusia ni

Quick links

Citations

44 review citations

Organization and regulation of gene transcription.
Cramer P. (2019)
43 more

12 mentions without citation

Structure and mechanism of the RNA polymerase II transcription machinery.
Schier et al. (2020)
11 more