9LN8 | pdb_00009ln8

Structure of NAP1 in complex with H2A.Z-H2B

• PDB DOI: https://doi.org/10.2210/pdb9LN8/pdb

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


• Deposited: 2025-01-21 Released: 2025-12-24 
• Deposition Author(s): Li, X., Li, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.258 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structure of NAP1 in complex with H2A.Z-H2B

Li, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 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

Macromolecule Content 

• Total Structure Weight: 92.46 kDa 
• Atom Count: 5,691 
• Modeled Residue Count: 716 
• Deposited Residue Count: 819 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome assembly protein 1-like 1	A, B	308	Caenorhabditis elegans	Mutation(s): 0  Gene Names: nap-1, CELE_D2096.8, D2096.8
UniProt
Find proteins for Q19007 (Caenorhabditis elegans) Explore Q19007  Go to UniProtKB:  Q19007

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H2A.Z-H2B	C [auth D]	203	Caenorhabditis elegans	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.258 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.852	α = 90
b = 79.257	β = 90
c = 175.112	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Li, X., Li, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release