5OKI

Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.293 

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Literature

Structural Basis for the Recruitment of Ctf18-RFC to the Replisome.

Grabarczyk, D.B.Silkenat, S.Kisker, C.

(2018) Structure 26: 137-144.e3

  • DOI: https://doi.org/10.1016/j.str.2017.11.004
  • Primary Citation of Related Structures:  
    5OKC, 5OKI

  • PubMed Abstract: 

    Ctf18-RFC is an alternative PCNA loader which plays important but poorly understood roles in multiple DNA replication-associated processes. To fulfill its specialist roles, the Ctf18-RFC clamp loader contains a unique module in which the Dcc1-Ctf8 complex is bound to the C terminus of Ctf18 (the Ctf18-1-8 module). Here, we report the structural and functional characterization of the heterotetrameric complex formed between Ctf18-1-8 and a 63 kDa fragment of DNA polymerase ɛ. Our data reveal that Ctf18-1-8 binds stably to the polymerase and far from its other functional sites, suggesting that Ctf18-RFC could be associated with Pol ɛ throughout normal replication as the leading strand clamp loader. We also show that Pol ɛ and double-stranded DNA compete to bind the same winged-helix domain on Dcc1, with Pol ɛ being the preferred binding partner, thus suggesting that there are two alternative pathways to recruit Ctf18-RFC to sites of replication.


  • Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany. Electronic address: daniel.grabarczyk@virchow.uni-wuerzburg.de.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit A
A, B
524Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: POL2DUN2YNL262WN0825
EC: 2.7.7.7
UniProt
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P21951
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UniProt GroupP21951
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sister chromatid cohesion protein DCC1C,
F [auth G]
380Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DCC1YCL016CYCL16C
UniProt
Find proteins for P25559 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome transmission fidelity protein 8D,
G [auth H]
133Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CTF8YHR191C
UniProt
Find proteins for P38877 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome transmission fidelity protein 18E,
H [auth I]
26Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CTF18CHL12YMR078CYM9582.03C
UniProt
Find proteins for P49956 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.293 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.678α = 90
b = 145.826β = 90
c = 378.752γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alexander von Humboldt FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references