› 7bp4

X-ray diffraction
2.1Å resolution

Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)

Released:
DOI: 10.2210/pdb7bp4/pdb
Model geometry
Fit model/data
PDB entry 7bp4 coloured by chain, front view.
PDB entry 7bp4 coloured by chain, side view.
PDB entry 7bp4 coloured by chain, top view.
Source organisms:
Primary publication:
NAP1-Related Protein 1 (NRP1) has multiple interaction modes for chaperoning histones H2A-H2B.
Luo Q, Wang B, Wu Z, Jiang W, Wang Y, Du K, Zhou N, Zheng L, Gan J, Shen WH, Ma J, Dong A
Proc Natl Acad Sci U S A 117 30391-30399 (2020)
PMID: 33199628

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-168059 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Histone H2A.6 Chains: A, G
Molecule details ›
Chains: A, G
Length: 93 amino acids
Theoretical weight: 10.03 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9LD28 (Residues: 14-106; Coverage: 72%)
Gene names: At5g54640, H2A-1, MRB17.14, RAT5
Sequence domains:
Histone H2B.1 Chains: B, H
Molecule details ›
Chains: B, H
Length: 98 amino acids
Theoretical weight: 11.03 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9LQQ4 (Residues: 51-148; Coverage: 66%)
Gene names: At1g07790, F24B9.10
Sequence domains: Core histone H2A/H2B/H3/H4
ASP-ASP-ASP-ASP-TYR Chains: C, L

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 61.748Å b: 62.248Å c: 130.692Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Structural comparisons reveal diverse binding modes between nucleosome assembly proteins and histones.
Gill et al. (2022)
1 more

2 mentions without citation

Dynamic structures of intrinsically disordered proteins related to the general transcription factor TFIIH, nucleosomes, and histone chaperones.
Okuda et al. (2022)
1 more

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO