28VY | pdb_000028vy

sCMGE assembled on ARS1 DNA with Sld2 and RPA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of the pre-initiation complex explains CMGE biogenesis.

Puhringer, T.Canal, B.Palm, G.Butryn, A.Couves, E.C.Willhoft, O.Lewis, J.S.Diffley, J.F.X.Costa, A.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10657-7
  • Primary Citation Related Structures: 
    28VY, 9RHI, 9RHJ, 9RHL, 9RHM

  • PubMed Abstract: 

    When cells enter S phase, bidirectional DNA replication is initiated through the kinase-regulated recruitment of three activators (Cdc45, GINS and Pol ε) to a duplex-DNA-loaded double hexamer of minichromosome maintenance (MCM) ATPases. Together, these proteins form two CMGE helicases that establish divergent replication forks as they become separated 1 . Here, to gain an understanding of CMGE biogenesis, we reconstituted the pre-initiation complex with purified yeast proteins. The cryo-electron-microscopy structure shows a set of firing factors caught in the act of assembling two symmetrical CMGEs. We show how stepwise complex formation reshapes MCM in preparation for DNA opening, and we explain how ATP promotes firing-factor ejection and CMGE maturation. We find that although Sld2 facilitates the recruitment of GINS to MCM, as expected, it also aids the efficient separation of the CMGE dimer, and is essential for the ejection of the lagging strand from MCM. These findings have direct implications for our understanding of the metazoan Sld2 orthologue, RECQL4, and point to a replication-fork establishment mechanism that is conserved across eukaryotes.


  • Organizational Affiliation
    • Macromolecular Machines Laboratory, Francis Crick Institute, London, UK.

Macromolecule Content 

  • Total Structure Weight: 1,147.98 kDa 
  • Atom Count: 54,130 
  • Modeled Residue Count: 6,684 
  • Deposited Residue Count: 9,998 
  • Unique protein chains: 13
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]1,006Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth C]217Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: PSF3YOL146W
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth D]294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5YDR489W
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control protein 45K [auth E]657Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45SLD4YLR103CL8004.11
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BL [auth F]689Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DPB2YPR175WP9705.7
UniProt
Find proteins for P24482 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AM [auth G]2,222Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL2DUN2YNL262WN0825
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1N [auth H]208Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF1YDR013WPZA208YD8119.18
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2O [auth I]213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF2YJL072CHRF213J1086
UniProt
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*CP*GP*AP*T)-3')G [auth A],
H [auth B]
27synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
BA [auth 6],
EA [auth 7],
T [auth 3],
V [auth 4],
Y [auth 5]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
R [auth 2]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CA [auth 6]
FA [auth 7]
GA [auth G]
HA [auth G]
Q [auth 2]
CA [auth 6],
FA [auth 7],
GA [auth G],
HA [auth G],
Q [auth 2],
W [auth 4],
Z [auth 5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth 6]
DA [auth 7]
P [auth 2]
S [auth 3]
U [auth 4]
AA [auth 6],
DA [auth 7],
P [auth 2],
S [auth 3],
U [auth 4],
X [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001065
The Francis Crick InstituteUnited KingdomFC001066
European Research Council (ERC)European Union820102
Boehringer Ingelheim Fonds (BIF)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release
  • Version 1.1: 2026-06-24
    Changes: Data collection, Database references
  • Version 1.2: 2026-07-01
    Changes: Data collection, Database references