› 5mlu

X-ray diffraction
2.8Å resolution

Crystal structure of the PFV GAG CBS bound to a mononucleosome

Released:
DOI: 10.2210/pdb5mlu/pdb
PDB entry 5mlu coloured by chain, front view.
PDB entry 5mlu coloured by chain, side view.
PDB entry 5mlu coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for spumavirus GAG tethering to chromatin.
Lesbats P, Serrao E, Maskell DP, Pye VE, O'Reilly N, Lindemann D, Engelman AN, Cherepanov P
Proc Natl Acad Sci U S A 114 5509-5514 (2017)
PMID: 28490494

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-119029 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 97 amino acids
Theoretical weight: 11.41 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 40-136; Coverage: 71%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 84 amino acids
Theoretical weight: 9.57 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 20-103; Coverage: 82%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 105 amino acids
Theoretical weight: 11.49 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 15-119; Coverage: 81%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chain: D
Molecule details ›
Chain: D
Length: 93 amino acids
Theoretical weight: 10.35 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 33-125; Coverage: 74%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H2B 1.1 Chain: H
Molecule details ›
Chain: H
Length: 94 amino acids
Theoretical weight: 10.48 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 32-125; Coverage: 75%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Gag protein Chain: M
Molecule details ›
Chain: M
Length: 17 amino acids
Theoretical weight: 1.99 KDa
Source organism: Simian foamy virus
Expression system: synthetic construct
UniProt:
  • Canonical: P14349 (Residues: 535-551; Coverage: 3%)
Gene name: gag
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.99 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.52 KDa

Ligands and Environments

1 bound ligand:
Ligand MN 4 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 107.26Å b: 109.45Å c: 175.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.208 0.252
Expression systems:
  • Escherichia coli
  • synthetic construct

Quick links

Citations

10 review citations

Control of Viral Latency by Episome Maintenance Proteins.
De Leo et al. (2020)
9 more

5 mentions without citation

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