9L06 | pdb_00009l06

The cryo-EM structure of ATRX in complex with the nucleosome in the ADP.BeFx-bound state (composite)

• PDB DOI: https://doi.org/10.2210/pdb9L06/pdb
• EM Map EMD-62690: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-12-11 Released: 2026-06-17 
• Deposition Author(s): Zhou, K., Duan, S., Liu, Y.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic insights into chromatin modulation by the orphan remodeler ATRX

Zhou, K., Liu, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A5B2C1D1 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 and generated by (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 378.11 kDa 
• Atom Count: 17,693 
• Modeled Residue Count: 1,784 
• Deposited Residue Count: 2,631 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	A, E	136	Homo sapiens	Mutation(s): 0  Gene Names: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243 GTEx:  ENSG00000132475 ENSG00000163041

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B	87	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-C	C, G	130	Homo sapiens	Mutation(s): 0  Gene Names: H2AC6, H2AFL, HIST1H2AC
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens) Explore Q93077  Go to UniProtKB:  Q93077
PHAROS:  Q93077 GTEx:  ENSG00000180573

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-C/E/F/G/I	D, H	126	Homo sapiens	Mutation(s): 0  Gene Names:  H2BC4, H2BFL, HIST1H2BC, H2BC6, H2BFH, HIST1H2BE, H2BC7, H2BFG, HIST1H2BF, H2BC8, H2BFA, HIST1H2BG, H2BC10, H2BFK, HIST1H2BI
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens) Explore P62807  Go to UniProtKB:  P62807
PHAROS:  P62807 GTEx:  ENSG00000180596 ENSG00000277224 ENSG00000278588 ENSG00000273802 ENSG00000274290

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	F	86	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator ATRX	K	1,260	Homo sapiens	Mutation(s): 0  Gene Names: ATRX, RAD54L, XH2 EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt)
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	Length	Organism	Image
DNA (207-MER)	I	207	Homo sapiens

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (207-MER)	J	207	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	L [auth K]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	M [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-17 
Deposition Author(s): Zhou, K., Duan, S., Liu, Y.

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	27122123

Revision History  

• Version 1.0: 2026-06-17
  Type: Initial release