5OKI | pdb_00005oki

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 (Depositor), 0.319 (DCC) 
  • R-Value Work: 
    0.293 (Depositor), 0.298 (DCC) 
  • R-Value Observed: 
    0.293 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 244.49 kDa 
  • Atom Count: 15,910 
  • Modeled Residue Count: 1,967 
  • Deposited Residue Count: 2,126 
  • Unique protein chains: 4

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 (PDB Primary Data), 3.1.11 (UniProt)
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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UniProt GroupP25559
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Reference Sequence
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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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Go to UniProtKB:  P38877
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UniProt GroupP38877
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Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore P49956 
Go to UniProtKB:  P49956
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UniProt GroupP49956
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free:  0.312 (Depositor), 0.319 (DCC) 
  • R-Value Work:  0.293 (Depositor), 0.298 (DCC) 
  • R-Value Observed: 0.293 (Depositor) 
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
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary