8TWA | pdb_00008twa

Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-PolE-DNA complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Mechanism of PCNA loading by Ctf18-RFC for leading-strand DNA synthesis.

Yuan, Z., Georgescu, R., Yao, N.Y., Yurieva, O., O'Donnell, M.E., Li, H.

(2024) Science 385: eadk5901-eadk5901

  • DOI: https://doi.org/10.1126/science.adk5901
  • Primary Citation Related Structures: 
    8TW7, 8TW8, 8TW9, 8TWA, 8TWB, 9B8R

  • PubMed Abstract: 

    The proliferating cell nuclear antigen (PCNA) clamp encircles DNA to hold DNA polymerases (Pols) to DNA for processivity. The Ctf18-RFC PCNA loader, a replication factor C (RFC) variant, is specific to the leading-strand Pol (Polε). We reveal here the underlying mechanism of Ctf18-RFC specificity to Polε using cryo-electron microscopy and biochemical studies. We found that both Ctf18-RFC and Polε contain specific structural features that direct PCNA loading onto DNA. Unlike other clamp loaders, Ctf18-RFC has a disordered ATPase associated with a diverse cellular activities (AAA+) motor that requires Polε to bind and stabilize it for efficient PCNA loading. In addition, Ctf18-RFC can pry prebound Polε off of DNA, then load PCNA onto DNA and transfer the PCNA-DNA back to Polε. These elements in both Ctf18-RFC and Polε provide specificity in loading PCNA onto DNA for Polε.

    • Organizational Affiliation: 
    • Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.

Macromolecule Content 

  • Total Structure Weight: 650.25 kDa 
  • Atom Count: 31,914 
  • Modeled Residue Count: 4,024 
  • Deposited Residue Count: 5,639 
  • Unique protein chains: 10
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromosome transmission fidelity protein 18A [auth C]26Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF18
UniProt
Find proteins for P49956 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AD [auth E]2,222Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL2, DUN2, YNL262W, N0825
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: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromosome transmission fidelity protein 8E [auth D]132Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF8
UniProt
Find proteins for P38877 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Sister chromatid cohesion protein DCC1F [auth B]380Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DCC1, YCL016C, YCL16C
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Replication factor C subunit 4G [auth 4]319Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC4
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Replication factor C subunit 3H [auth 3]327Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC3
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Replication factor C subunit 2I [auth 2]340Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC2
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Replication factor C subunit 5J [auth 5]354Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC5
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromosome transmission fidelity protein 18K [auth 1]741Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF18, CHL12, YMR078C, YM9582.03C
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigenL [auth X],
M [auth Y],
N [auth Z]		258Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL30, YBR088C, YBR0811
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
Primer DNAB [auth P]9synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
Template DNAC [auth T]15synthetic construct
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Reference Sequence

Small Molecules

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

Query on AGS


Download:Ideal Coordinates CCD File
P [auth 4],
R [auth 3],
T [auth 2]		PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP

Query on ADP


Download:Ideal Coordinates CCD File
V [auth 5]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
O [auth E]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
Q [auth 4],
S [auth 3],
U [auth 2]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115809
Howard Hughes Medical Institute (HHMI)United StatesM.E.O.

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary