8SIY

Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A dual role for the chromatin reader ORCA/LRWD1 in targeting the origin recognition complex to chromatin.

Sahu, S.Ekundayo, B.E.Kumar, A.Bleichert, F.

(2023) EMBO J 42: e114654-e114654

  • DOI: https://doi.org/10.15252/embj.2023114654
  • Primary Citation of Related Structures:  
    8SIU, 8SIY

  • PubMed Abstract: 

    Eukaryotic cells use chromatin marks to regulate the initiation of DNA replication. The origin recognition complex (ORC)-associated protein ORCA plays a critical role in heterochromatin replication in mammalian cells by recruiting the initiator ORC, but the underlying mechanisms remain unclear. Here, we report crystal and cryo-electron microscopy structures of ORCA in complex with ORC's Orc2 subunit and nucleosomes, establishing that ORCA orchestrates ternary complex assembly by simultaneously recognizing a highly conserved peptide sequence in Orc2, nucleosomal DNA, and repressive histone trimethylation marks through an aromatic cage. Unexpectedly, binding of ORCA to nucleosomes prevents chromatin array compaction in a manner that relies on H4K20 trimethylation, a histone modification critical for heterochromatin replication. We further show that ORCA is necessary and sufficient to specifically recruit ORC into chromatin condensates marked by H4K20 trimethylation, providing a paradigm for studying replication initiation in specific chromatin contexts. Collectively, our findings support a model in which ORCA not only serves as a platform for ORC recruitment to nucleosomes bearing specific histone marks but also helps establish a local chromatin environment conducive to subsequent MCM2-7 loading.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat and WD repeat-containing protein 1651Rattus norvegicusMutation(s): 0 
Gene Names: Lrwd1
UniProt
Find proteins for A0A140UHX1 (Rattus norvegicus)
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Go to UniProtKB:  A0A140UHX1
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UniProt GroupA0A140UHX1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2B [auth C],
F [auth G]
135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth D],
G [auth H]
102Xenopus laevisMutation(s): 0 
Gene Names: LOC121398084
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AD [auth E],
H [auth I]
129Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2BE [auth F],
I [auth J]
122Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2L [auth B]103Rattus norvegicusMutation(s): 0 
Gene Names: Orc2Orc2l
UniProt
Find proteins for Q75PQ8 (Rattus norvegicus)
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UniProt GroupQ75PQ8
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Entity ID: 6
MoleculeChains LengthOrganismImage
Widom 601 DNAJ [auth K]153synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
Widom 601 DNAK [auth L]153synthetic construct
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ML3
Query on ML3
C [auth D],
G [auth H]
L-PEPTIDE LINKINGC8 H19 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM141313
European Research Council (ERC)European UnionERC-STG-757909

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-27
    Changes: Database references
  • Version 1.3: 2023-11-15
    Changes: Data collection