› 6om3

X-ray diffraction
3.3Å resolution

Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle

Released:
DOI: 10.2210/pdb6om3/pdb
PDB entry 6om3 coloured by chain, front view.
PDB entry 6om3 coloured by chain, side view.
PDB entry 6om3 coloured by chain, top view.
Source organisms:
Primary publication:
Structure and function of the Orc1 BAH-nucleosome complex.
De Ioannes P, Leon VA, Kuang Z, Wang M, Boeke JD, Hochwagen A, Armache KJ
Nat Commun 10 2894 (2019)
PMID: 31263106

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-120395 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.2 Chains: A, E, M, Q
Molecule details ›
Chains: A, E, M, Q
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F, N, R
Molecule details ›
Chains: B, F, N, R
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 type 1 Chains: C, G, O, S
Molecule details ›
Chains: C, G, O, S
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Histone H2B 1.1 Chains: D, H, P, T
Molecule details ›
Chains: D, H, P, T
Length: 126 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Origin recognition complex subunit 1 Chains: K, L, W, X
Molecule details ›
Chains: K, L, W, X
Length: 224 amino acids
Theoretical weight: 26.07 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P54784 (Residues: 2-214; Coverage: 23%)
Gene names: ORC1, YML065W
Sequence domains: BAH domain
DNA (146-MER) Chains: I, U
Molecule details ›
Chains: I, U
Length: 146 nucleotides
Theoretical weight: 44.82 KDa
DNA (147-MER) Chains: J, V
Molecule details ›
Chains: J, V
Length: 147 nucleotides
Theoretical weight: 45.61 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 100.254Å b: 166.428Å c: 168.277Å
α: 90° β: 90.28° γ: 90°
R-values:
R R work R free
0.217 0.213 0.25
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda

Quick links

Citations

1 review citation

Getting there: understanding the chromosomal recruitment of the AAA+ ATPase Pch2/TRIP13 during meiosis.
Cardoso da Silva et al. (2021)
13 other articles

2 mentions without citation

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
1 more