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

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
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This is version 1.1 of the entry. See complete history.

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) Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai)

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

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

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome Assembly Protein	A B C [auth E] D [auth F] G [auth C] 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q19007
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6AZJ8
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02281
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.