23AK | pdb_000023ak

Cryo-EM structure of ATRX ATPase domain bound to a nucleosome

• PDB DOI: https://doi.org/10.2210/pdb23AK/pdb
• EM Map EMD-68803: EMDB EMDataResource

• Classification: NUCLEAR PROTEIN
• Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-01-29 Released: 2026-10-28 
• Deposition Author(s): Huang, Y., Wang, X., Chen, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Structural basis for the non-canonical nucleosome remodeling by ATRX

Wang, X., Yan, S., Huang, Y., Ge, K., Wu, Y., Xu, W., Kang, Y., Yao, D., Liu, X., Chen, Y.

(2026) Mol Cell 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 293.51 kDa 
• Atom Count: 16,858 
• Modeled Residue Count: 1,670 
• Deposited Residue Count: 2,093 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	A [auth B], C [auth F]	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	B [auth C], D [auth G]	129	Xenopus laevis	Mutation(s): 0  Gene Names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8  Go to UniProtKB:  Q6AZJ8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin remodeler ATRX	G [auth K]	817	Homo sapiens	Mutation(s): 0  Gene Names: ATRX, RAD54L, XH2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P46100 (Homo sapiens) Explore P46100  Go to UniProtKB:  P46100
PHAROS:  P46100 GTEx:  ENSG00000085224

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	H [auth A], J [auth E]	135	Xenopus laevis	Mutation(s): 0  Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1  Go to UniProtKB:  A0A310TTQ1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	I [auth D], K [auth H]	125	Xenopus laevis	Mutation(s): 0  Gene Names: LOC108704303
UniProt
Find proteins for A0A8J0U496 (Xenopus laevis) Explore A0A8J0U496  Go to UniProtKB:  A0A8J0U496

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	E [auth I]	147	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	F [auth J]	147	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC	4.6.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Huang, Y., Wang, X., Chen, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2023YFA1800403

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release