9T4V | pdb_00009t4v

ALC1/CHD1L in an intermediate conformation, bound to a PARylated nucleosome


Experimental Data Snapshot

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

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure of ALC1 in an open conformation bound to a PARylated nucleosome.

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

(2026) Acta Crystallogr D Struct Biol 

  • DOI: https://doi.org/10.1107/S2059798326004158
  • Primary Citation Related Structures: 
    9T4V

  • PubMed Abstract: 

    Nucleosomes are the repeating unit of chromatin. They act as recognition platforms for chromatin-binding factors that coordinate genome maintenance. The chromatin remodeler Amplified in Liver Cancer 1 (ALC1) is a key component of the DNA-damage response and a promising therapeutic target in cancer. Through extensive classification of our previously deposited cryo-electron microscopy dataset, we identified a previously unresolved ALC1-nucleosome complex characterized by a more open conformation of ALC1. This is the first structure of ALC1 in which all domains are visualized in the context of a nucleosome complex, including the regulatory macro domain and a single α-helix motif within the linker. This newly identified conformation may represent an intermediate between the auto-inhibited and active states, and provides new structural insights into the conformational transitions that regulate the activity of ALC1.


  • Organizational Affiliation
    • Structura Biotechnology Inc., Toronto, Ontario, Canada.

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


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
136Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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UniProt GroupP84233
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
130Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
Go to UniProtKB:  P06897
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UniProt GroupP06897
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
123Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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UniProt GroupP02281
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromodomain-helicase-DNA-binding protein 1-like872Homo sapiensMutation(s): 0 
Gene Names: CHD1LALC1
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 
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UniProt GroupQ86WJ1
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
Widom 601 sequence160synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
Widom 601 sequence160synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2-5419
RECONSTRUCTIONcryoSPARC4.7.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Data collection, Structure summary
  • Version 1.2: 2026-05-27
    Changes: Data collection, Database references