9I3I | pdb_00009i3i

Cryo-EM structure of the MCM-ORC (MO) complex featuring an ORC2 regulatory domain involved in cell cycle regulation of MCM-DH loading for DNA replication.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9I3I

This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6RQC

Literature

Cell cycle regulation has shaped replication origins in budding yeast.

Lim, C.T.Miller, T.C.R.Tan, K.W.Talele, S.Early, A.East, P.Sanchez, H.Dekker, N.H.Costa, A.Diffley, J.F.X.

(2025) Nat Struct Mol Biol 32: 1697-1707

  • DOI: https://doi.org/10.1038/s41594-025-01591-9
  • Primary Citation Related Structures: 
    8RIF, 8RIG, 9I3I

  • PubMed Abstract: 

    Eukaryotic DNA replication initiates from genomic loci known as origins. At budding yeast origins like ARS1, a double hexamer (DH) of the MCM replicative helicase is assembled by origin recognition complex (ORC), Cdc6 and Cdt1 by sequential hexamer loading from two opposed ORC binding sites. Cyclin-dependent kinase (CDK) inhibits DH assembly, which prevents re-replication by restricting helicase loading to the G1 phase. Here, we show that an intrinsically disordered region (IDR) in the Orc2 subunit promotes interaction between ORC and the first loaded, closed-ring MCM hexamer (the MCM-ORC (MO) intermediate). CDK-dependent phosphorylation of this IDR blocks MO formation and DH assembly. We show that MO stabilizes ORC at lower-affinity binding sites required for second hexamer loading. Origins comprising two high-affinity ORC sites can assemble DH efficiently without MO by independently loading single hexamers. Strikingly, these origins escape CDK inhibition in vitro and in vivo. Our work reveals mechanistic plasticity in MCM loading with implications for understanding how CDK regulation has shaped yeast origin evolution and how natural, strong origins might escape cell cycle regulation. We also identify key steps common to loading pathways, with implications for understanding how MCM is loaded in other eukaryotes.


  • Organizational Affiliation
    • Chromosome Replication Laboratory, The Francis Crick Institute, London, UK.

Macromolecule Content 

  • Total Structure Weight: 1,086.94 kDa 
  • Atom Count: 53,583 
  • Modeled Residue Count: 6,392 
  • Deposited Residue Count: 9,248 
  • Unique protein chains: 12
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 1949Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC1YML065W
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2620Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC2RRR1SIR5YBR060CYBR0523
UniProt
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 3616Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC3OAF1OIF1YLL004WL1365
UniProt
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 4529Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC4YPR162CP9325.5
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 5479Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC5YNL261WN0834
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 6435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC6AAP1YHR118C
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2G [auth 2]868Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3H [auth 3]1,006Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4I [auth 4]933Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5J [auth 5]775Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6K [auth 6]1,017Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7L [auth 7]845Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (88-MER)M [auth X]88Saccharomyces cerevisiae S288C
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Reference Sequence
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (88-MER)N [auth Y]88Saccharomyces cerevisiae S288C
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
O [auth A],
Q [auth D],
S [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
BA [auth 7],
U [auth 2],
W [auth 3],
Y [auth 5]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth 6],
CA [auth 7],
V [auth 2],
X [auth 4],
Z [auth 5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
P [auth A],
R [auth D],
T [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomFC0010065
Medical Research Council (MRC, United Kingdom)United KingdomFC0010065
Cancer Research UKUnited KingdomFC0010065
European Research Council (ERC)European Union820102
Novo Nordisk FoundationDenmarkNNF22OC0073571
The Carlsberg FoundationDenmarkCF21_0571

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Database references
  • Version 1.2: 2025-10-01
    Changes: Database references