› 7unc

Electron Microscopy
3Å resolution

Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome

Released:
DOI: 10.2210/pdb7unc/pdb
PDB entry 7unc coloured by chain, front view.
PDB entry 7unc coloured by chain, side view.
PDB entry 7unc coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of nucleosome retention during transcription elongation.
Filipovski M, Soffers JHM, Vos SM, Farnung L
Science 376 1313-1316 (2022)
PMID: 35709268
Related structures: EMD-26620

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 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-105088 (preferred)
Entry contents:
25 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (28 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: A0A4X1TVZ5 (Residues: 1-1251; Coverage: 100%)
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: A0A481DF93 (Residues: 46-320; Coverage: 86%)
Sequence domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 184 amino acids
Theoretical weight: 20.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1GCS3 (Residues: 1-184; Coverage: 100%)
Sequence domains: RNA polymerase Rpb4
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: A0A4X1VTX4 (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: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase subunit Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VKG7 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
Sequence domains:
RPB8 Chain: H
Molecule details ›
Chain: H
Length: 150 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
RPB9 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 14.54 KDa
Source organism: Sus scrofa
RPB10 Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
RPB11 Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Sus scrofa
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
Transcription elongation factor SPT6 Chain: M
Molecule details ›
Chain: M
Length: 1729 amino acids
Theoretical weight: 199.6 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7KZ85 (Residues: 1-1726; Coverage: 100%)
Gene names: KIAA0162, SPT6H, SUPT6H
Sequence domains:
Transcription elongation factor A protein 1 Chain: O
Molecule details ›
Chain: O
Length: 304 amino acids
Theoretical weight: 34.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23193 (Residues: 1-301; Coverage: 100%)
Gene names: GTF2S, TCEA1, TFIIS
Sequence domains:
RNA polymerase-associated protein CTR9 homolog Chain: Q
Molecule details ›
Chain: Q
Length: 1179 amino acids
Theoretical weight: 134.51 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6PD62 (Residues: 1-1173; Coverage: 100%)
Gene names: CTR9, KIAA0155, SH2BP1
Sequence domains:
RNA polymerase-associated protein RTF1 homolog Chain: R
Molecule details ›
Chain: R
Length: 713 amino acids
Theoretical weight: 80.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92541 (Residues: 1-710; Coverage: 100%)
Gene names: KIAA0252, RTF1
Sequence domains: Plus-3 domain
RNA polymerase-associated protein LEO1 Chain: U
Molecule details ›
Chain: U
Length: 666 amino acids
Theoretical weight: 75.51 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: 531 amino acids
Theoretical weight: 60.05 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
Parafibromin Chain: X
Molecule details ›
Chain: X
Length: 531 amino acids
Theoretical weight: 60.67 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6P1J9 (Residues: 1-531; Coverage: 100%)
Gene names: C1orf28, CDC73, HRPT2
Sequence domains:
Transcription elongation factor SPT5 Chain: Z
Molecule details ›
Chain: Z
Length: 1087 amino acids
Theoretical weight: 121.23 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O00267 (Residues: 1-1087; Coverage: 100%)
Gene names: SPT5, SPT5H, SUPT5H
Sequence domains:
Histone H3.2 Chains: a, e
Molecule details ›
Chains: a, e
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: b, f
Molecule details ›
Chains: b, f
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A Chains: c, g
Molecule details ›
Chains: c, g
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 1-130; Coverage: 100%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Histone H2B 1.1 Chains: d, h
Molecule details ›
Chains: d, h
Length: 123 amino acids
Theoretical weight: 13.66 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Non-template DNA Chain: N
Molecule details ›
Chain: N
Length: 209 nucleotides
Theoretical weight: 64.76 KDa
Template DNA Chain: T
Molecule details ›
Chain: T
Length: 215 nucleotides
Theoretical weight: 66.19 KDa
RNA Chain: P
Molecule details ›
Chain: P
Length: 16 nucleotides
Theoretical weight: 5 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
2 modified residues:
Ligand TPO 2 x TPO
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-26620
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

5 review citations

Are extraordinary nucleosome structures more ordinary than we thought?
Chong et al. (2023)
4 more

1 mention without citation

Structural Transition of the Nucleosome during Transcription Elongation.
Kujirai et al. (2023)