6ZHX

Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Mechanistic Insights into Regulation of the ALC1 Remodeler by the Nucleosome Acidic Patch.

Lehmann, L.C.Bacic, L.Hewitt, G.Brackmann, K.Sabantsev, A.Gaullier, G.Pytharopoulou, S.Degliesposti, G.Okkenhaug, H.Tan, S.Costa, A.Skehel, J.M.Boulton, S.J.Deindl, S.

(2020) Cell Rep 33: 108529-108529

  • DOI: https://doi.org/10.1016/j.celrep.2020.108529
  • Primary Citation of Related Structures:  
    6ZHX, 6ZHY

  • PubMed Abstract: 

    Upon DNA damage, the ALC1/CHD1L nucleosome remodeling enzyme (remodeler) is activated by binding to poly(ADP-ribose). How activated ALC1 recognizes the nucleosome, as well as how this recognition is coupled to remodeling, is unknown. Here, we show that remodeling by ALC1 requires a wild-type acidic patch on the entry side of the nucleosome. The cryo-electron microscopy structure of a nucleosome-ALC1 linker complex reveals a regulatory linker segment that binds to the acidic patch. Mutations within this interface alter the dynamics of ALC1 recruitment to DNA damage and impede the ATPase and remodeling activities of ALC1. Full activation requires acidic patch-linker segment interactions that tether the remodeler to the nucleosome and couple ATP hydrolysis to nucleosome mobilization. Upon DNA damage, such a requirement may be used to modulate ALC1 activity via changes in the nucleosome acidic patches.


  • Organizational Affiliation

    Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
136Xenopus laevisMutation(s): 1 
Gene Names: XELAEV_18002543mg
UniProt
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
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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)
Explore P62799 
Go to UniProtKB:  P62799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62799
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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)
Go to UniProtKB:  P06897
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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)
Go to UniProtKB:  P02281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chromodomain-helicase-DNA-binding protein 1-like
K, L
37Homo sapiensMutation(s): 0 
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WJ1 (Homo sapiens)
Go to UniProtKB:  Q86WJ1
PHAROS:  Q86WJ1
GTEx:  ENSG00000131778 
Sequence Annotations
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-MER) Widom 601 sequence145synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER) Widom 601 sequence145synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTISOLDE1.0b5

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)SwedenChromatinRemodeling

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 2.0: 2021-07-14
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2024-07-10
    Changes: Data collection, Database references, Refinement description