› 3mvd

X-ray diffraction
2.9Å resolution

Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle

Released:
DOI: 10.2210/pdb3mvd/pdb
PDB entry 3mvd coloured by chain, front view.
PDB entry 3mvd coloured by chain, side view.
PDB entry 3mvd coloured by chain, top view.
Source organisms:
Primary publication:
Structure of RCC1 chromatin factor bound to the nucleosome core particle.
Makde RD, England JR, Yennawar HP, Tan S
Nature 467 562-6 (2010)
PMID: 20739938

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-116591 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
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
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 2-130; Coverage: 99%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.52 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
Structure domains: Histone, subunit A
Regulator of chromosome condensation Chains: K, L
Molecule details ›
Chains: K, L
Length: 423 amino acids
Theoretical weight: 45.37 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P25171 (Residues: 2-422; Coverage: 77%)
Gene names: Bj1, CG10480, Rcc1
Sequence domains: Regulator of chromosome condensation (RCC1) repeat
Structure domains: Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II
DNA (146-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.14 KDa
DNA (146-MER) Chain: J
Molecule details ›
Chain: J
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-E
Spacegroup: P21
Unit cell:
a: 102.681Å b: 183.036Å c: 107.03Å
α: 90° β: 101.52° γ: 90°
R-values:
R R work R free
0.176 0.175 0.216
Expression system: Escherichia coli

Quick links

Citations

48 review citations

Regulation of small GTPases by GEFs, GAPs, and GDIs.
Cherfils et al. (2013)
47 more

46 mentions without citation

Nucleosome structure and function.
McGinty et al. (2015)
45 more