9T4V | pdb_00009t4v

Activation intermediate of ALC1/CHD1L bound to a PARylated nucleosome

• PDB DOI: https://doi.org/10.2210/pdb9T4V/pdb
• NAKB: 9T4V
• EM Map EMD-55533: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-11-02 Released: 2025-11-19 
• Deposition Author(s): Bridges, H.R., Bacic, L., Deindl, S., Gaullier, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Activation intermediate of ALC1/CHD1L bound to a PARylated nucleosome

Bridges, H.R., Bacic, L., Deindl, S., Gaullier, G.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.11.10.687450

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A7B1C1 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: 306.81 kDa 
• Atom Count: 18,913 
• Modeled Residue Count: 1,908 
• Deposited Residue Count: 2,176 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	136	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	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 type 1	C, G	130	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	123	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain-helicase-DNA-binding protein 1-like	K	872	Homo sapiens	Mutation(s): 0  Gene Names: CHD1L, ALC1 EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WJ1 (Homo sapiens) Explore Q86WJ1  Go to UniProtKB:  Q86WJ1
PHAROS:  Q86WJ1 GTEx:  ENSG00000131778

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Widom 601 sequence	I	160	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Widom 601 sequence	J	160	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2-5419
RECONSTRUCTION	cryoSPARC	4.7.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Bridges, H.R., Bacic, L., Deindl, S., Gaullier, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release