9EAR | pdb_00009ear

CHD1-nucleosome complex (closed state)

• PDB DOI: https://doi.org/10.2210/pdb9EAR/pdb
• EM Map EMD-47841: EMDB EMDataResource

• Classification: TRANSLOCASE
• Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2024-11-11 Released: 2025-05-07 
• Deposition Author(s): James, A.M., Farnung, L.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of human CHD1 nucleosome recruitment and pausing

James, A.M., Farnung, L.

(2025) Mol Cell 

• DOI: https://doi.org/10.1016/j.molcel.2025.04.020

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A8B1 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: electron microscopy

Macromolecule Content

• Total Structure Weight: 344.68 kDa 
• Atom Count: 18,004 
• Modelled Residue Count: 1,738 
• Deposited Residue Count: 2,489 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	136	Xenopus laevis	Mutation(s): 1  Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1  Go to UniProtKB:  A0A310TTQ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	86	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	105	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	95	Xenopus laevis	Mutation(s): 0  Gene Names: XELAEV_18032685mg
UniProt
Find proteins for A0A1L8FQA5 (Xenopus laevis) Explore A0A1L8FQA5  Go to UniProtKB:  A0A1L8FQA5

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain-helicase-DNA-binding protein 1	K [auth W]	1,329	Homo sapiens	Mutation(s): 0  Gene Names: CHD1 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for O14646 (Homo sapiens) Explore O14646  Go to UniProtKB:  O14646
PHAROS:  O14646 GTEx:  ENSG00000153922

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (205-MER)	I	158	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (205-MER)	J	158	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	L [auth W]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF	M [auth W]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ML3	A, E	L-PEPTIDE LINKING	C8 H19 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): James, A.M., Farnung, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	ES036404

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release