8ZP4 | pdb_00008zp4

Cryo-EM structure of origin recognition complex (Orc1 to 5) with ARS1 DNA bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

DNA bending mediated by ORC is essential for replication licensing in budding yeast.

Lam, W.H.Yu, D.Zhang, Q.Lin, Y.Li, N.Li, J.Wu, Y.Zhang, Y.Gao, N.Tye, B.K.Zhai, Y.Dang, S.

(2025) Proc Natl Acad Sci U S A 122: e2502277122-e2502277122

  • DOI: https://doi.org/10.1073/pnas.2502277122
  • Primary Citation of Related Structures:  
    8ZP4, 8ZP5, 8ZPK

  • PubMed Abstract: 

    In eukaryotes, the origin recognition complex (ORC) promotes the assembly of minichromosome maintenance 2 to 7 complexes into a head-to-head double hexamer at origin DNA in a process known as replication licensing. In this study, we present a series of cryoelectron microscopy structures of yeast ORC mutants in complex with origin DNA. We show that Orc6, the smallest subunit of ORC, utilizes its transcription factor II B-B domain to orchestrate the sequential binding of ORC to origin DNA. In addition, Orc6 plays the role of a scaffold by stabilizing the basic patch (BP) of Orc5 for ORC to capture and bend origin DNA. Importantly, disrupting DNA bending through mutating three key residues in Orc5-BP impairs ORC's ability to promote replication initiation at two points during the pre-RC assembly process. This study dissects the multifaceted role of Orc6 in orchestrating ORC's activities on DNA and underscores the vital role of DNA bending by ORC in replication licensing.


  • Organizational Affiliation
    • Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 1914Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC1
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54784 
Go to UniProtKB:  P54784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54784
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2620Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC2
UniProt
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32833 
Go to UniProtKB:  P32833
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32833
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 3616Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC3
UniProt
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54790 
Go to UniProtKB:  P54790
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54790
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 4529Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC4
UniProt
Find proteins for P54791 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54791 
Go to UniProtKB:  P54791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54791
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 5G [auth E]479Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC5
UniProt
Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50874 
Go to UniProtKB:  P50874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50874
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (31-MER)E [auth G]77Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (31-MER)F [auth H]77Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19-4092
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release