8OUW

Cryo-EM structure of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 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

DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in Caenorhabditis elegans.

Xia, Y.Sonneville, R.Jenkyn-Bedford, M.Ji, L.Alabert, C.Hong, Y.Yeeles, J.T.P.Labib, K.P.M.

(2023) Science 381: eadi4932-eadi4932

  • DOI: https://doi.org/10.1126/science.adi4932
  • Primary Citation of Related Structures:  
    8OUW

  • PubMed Abstract: 

    Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that are not present in yeast. In this work, we show that Caenorhabditis elegans DNSN-1, the ortholog of human DONSON, functions during helicase assembly in a complex with MUS-101/TOPBP1. DNSN-1 is required to recruit the GINS complex to chromatin, and a cryo-electron microscopy structure indicates that DNSN-1 positions GINS on the MCM-2-7 helicase motor (comprising the six MCM-2 to MCM-7 proteins), by direct binding of DNSN-1 to GINS and MCM-3, using interfaces that we show are important for initiation and essential for viability. These findings identify DNSN-1 as a missing link in our understanding of DNA replication initiation, suggesting that initiation defects underlie the human disease syndrome that results from DONSON mutations.


  • Organizational Affiliation

    The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]881Caenorhabditis elegansMutation(s): 0 
Gene Names: mcm-2CELE_Y17G7B.5Y17G7B.5
EC: 3.6.4.12
UniProt
Find proteins for Q9XXI9 (Caenorhabditis elegans)
Explore Q9XXI9 
Go to UniProtKB:  Q9XXI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XXI9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]812Caenorhabditis elegansMutation(s): 0 
Gene Names: mcm-3C25D7.6CELE_C25D7.6
EC: 3.6.4.12
UniProt
Find proteins for Q9XVR7 (Caenorhabditis elegans)
Explore Q9XVR7 
Go to UniProtKB:  Q9XVR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XVR7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor mcm-4C [auth 4]823Caenorhabditis elegansMutation(s): 0 
Gene Names: mcm-4let-358lin-6Y39G10AR.14
EC: 3.6.4.12
UniProt
Find proteins for Q95XQ8 (Caenorhabditis elegans)
Explore Q95XQ8 
Go to UniProtKB:  Q95XQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95XQ8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor mcm-5D [auth 5]759Caenorhabditis elegansMutation(s): 0 
Gene Names: mcm-5R10E4.4
EC: 3.6.4.12
UniProt
Find proteins for Q21902 (Caenorhabditis elegans)
Explore Q21902 
Go to UniProtKB:  Q21902
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ21902
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor mcm-6E [auth 6]810Caenorhabditis elegansMutation(s): 0 
Gene Names: mcm-6ZK632.1
EC: 3.6.4.12
UniProt
Find proteins for P34647 (Caenorhabditis elegans)
Explore P34647 
Go to UniProtKB:  P34647
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34647
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]730Caenorhabditis elegansMutation(s): 0 
Gene Names: mcm-7MCM7CELE_F32D1.10F32D1.10
EC: 3.6.4.12
UniProt
Find proteins for O16297 (Caenorhabditis elegans)
Explore O16297 
Go to UniProtKB:  O16297
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO16297
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Probable DNA replication complex GINS protein PSF1G [auth A]205Caenorhabditis elegansMutation(s): 0 
Gene Names: psf-1R53.6
UniProt
Find proteins for Q22019 (Caenorhabditis elegans)
Explore Q22019 
Go to UniProtKB:  Q22019
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ22019
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Probable DNA replication complex GINS protein PSF2H [auth B]180Caenorhabditis elegansMutation(s): 0 
Gene Names: psf-2F31C3.5
UniProt
Find proteins for O62193 (Caenorhabditis elegans)
Explore O62193 
Go to UniProtKB:  O62193
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO62193
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth C]193Caenorhabditis elegansMutation(s): 0 
Gene Names: psf-3CELE_Y65B4BR.8Y65B4BR.8
UniProt
Find proteins for Q9BL54 (Caenorhabditis elegans)
Explore Q9BL54 
Go to UniProtKB:  Q9BL54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BL54
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth D]224Caenorhabditis elegansMutation(s): 0 
Gene Names: sld-5CELE_Y113G7B.24Y113G7B.24
UniProt
Find proteins for Q9U2W9 (Caenorhabditis elegans)
Explore Q9U2W9 
Go to UniProtKB:  Q9U2W9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U2W9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45 homologK [auth E]574Caenorhabditis elegansMutation(s): 0 
Gene Names: evl-18CELE_F34D10.2F34D10.2
UniProt
Find proteins for Q7JMR0 (Caenorhabditis elegans)
Explore Q7JMR0 
Go to UniProtKB:  Q7JMR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7JMR0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Downstream Neighbor of SoN homologL [auth F],
M [auth G],
N [auth H]
594Caenorhabditis elegansMutation(s): 0 
Gene Names: dnsn-1C24H12.5CELE_C24H12.5
UniProt
Find proteins for H1ZUV7 (Caenorhabditis elegans)
Explore H1ZUV7 
Go to UniProtKB:  H1ZUV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH1ZUV7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Protein timeless homologQ [auth K]1,353Caenorhabditis elegansMutation(s): 0 
Gene Names: tim-1csg-5Y75B8A.22
UniProt
Find proteins for G5EDN3 (Caenorhabditis elegans)
Explore G5EDN3 
Go to UniProtKB:  G5EDN3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5EDN3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Protein TIPIN homologR [auth L]237Caenorhabditis elegansMutation(s): 0 
Gene Names: tipn-1F23C8.9
UniProt
Find proteins for Q9TXI0 (Caenorhabditis elegans)
Explore Q9TXI0 
Go to UniProtKB:  Q9TXI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9TXI0
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains LengthOrganismImage
DNA Leading Strand TemplateO [auth I],
P [auth J]
85Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
DNA Lagging Strand TemplateS [auth M]61Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
CA [auth 6],
DA [auth 7],
V [auth 3],
X [auth 4]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth 6],
FA [auth 7],
T [auth 2],
Y [auth 4],
Z [auth 5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth 6],
EA [auth 7],
U [auth 3],
W [auth 4]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--
Cancer Research UKUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Database references
  • Version 1.2: 2023-08-30
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Database references