6vz4

Electron Microscopy
3.9Å resolution

Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-120791 (preferred)
Entry contents:
8 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (10 distinct):
Histone H3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.41 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q92133 (Residues: 1-136; Coverage: 100%)
Gene names: H3l, Hist1h3f, h3, h3.2a, h3c8, h3c8.S, h3r, hist1h3g, hist1h3g.L, hist2h3, hist2h3c
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 BL21
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 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 BL21
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.81 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P02281 (Residues: 1-125; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Nuclear protein STH1/NPS1 Chain: K
Molecule details ›
Chain: K
Length: 813 amino acids
Theoretical weight: 95.11 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P32597 (Residues: 301-1097; Coverage: 59%)
Gene names: NPS1, STH1, YIL126W
Sequence domains:
Actin-related protein 7 Chain: L
Molecule details ›
Chain: L
Length: 477 amino acids
Theoretical weight: 53.86 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12406 (Residues: 1-477; Coverage: 100%)
Gene names: ARP7, SWP61, YP9367.14, YPR034W
Sequence domains: Actin
Actin-like protein ARP9 Chain: M
Molecule details ›
Chain: M
Length: 467 amino acids
Theoretical weight: 53.13 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q05123 (Residues: 1-467; Coverage: 100%)
Gene names: ARP9, SWP59, YM9973.07, YMR033W
Sequence domains: Actin
Regulator of Ty1 transposition protein 102 Chain: N
Molecule details ›
Chain: N
Length: 157 amino acids
Theoretical weight: 17.82 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P53330 (Residues: 1-157; Coverage: 100%)
Gene names: G9378, RTT102, YGR275W
Sequence domains: Rtt102p-like transcription regulator protein
DNA (185-MER) Chain: I
Molecule details ›
Chain: I
Length: 185 nucleotides
Theoretical weight: 56.84 KDa
DNA (185-MER) Chain: J
Molecule details ›
Chain: J
Length: 185 nucleotides
Theoretical weight: 57.4 KDa

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-21484
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli