8XAA | pdb_00008xaa

Structure of NAP1 in complex with H2A-H2B

• PDB DOI: https://doi.org/10.2210/pdb8XAA/pdb

• Classification: CHAPERONE
• Organism(s): Caenorhabditis elegans, Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-03 Released: 2024-12-04 
• Deposition Author(s): Xu, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structural insights into H2A-H2B and H2A.Z-H2B sliding on histone chaperone NAP1

Xu, L., Zhang, J., Wang, Y., Liu, D., Zeng, C., Chen, J., Pan, X.

(2025) Acta Biochim Biophys Sinica 

• DOI: https://doi.org/10.3724/abbs.2025241

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 322.51 kDa 
• Atom Count: 19,338 
• Modeled Residue Count: 2,448 
• Deposited Residue Count: 2,846 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome Assembly Protein	A, B, C [auth E], D [auth F], G [auth C], H [auth D], I [auth G], J [auth H]	308	Caenorhabditis elegans	Mutation(s): 0  Gene Names: nap-1
UniProt
Find proteins for Q19007 (Caenorhabditis elegans) Explore Q19007  Go to UniProtKB:  Q19007

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	E [auth I], K	92	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8  Go to UniProtKB:  Q6AZJ8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	F [auth J], L	99	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.489	α = 104.1
b = 92.926	β = 106.24
c = 119.354	γ = 94.18

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Xu, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release
  
• Version 1.1: 2025-12-24
  Changes: Database references, Structure summary