8TWB | pdb_00008twb

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

PDB DOI: https://doi.org/10.2210/pdb8TWB/pdb
EM Map EMD-41665: EMDB EMDataResource
NAKB: 8TWB

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Saccharomyces cerevisiae, synthetic construct
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2023-08-20 Released: 2024-09-04
Deposition Author(s): Yuan, Z., Georgescu, R., O'Donnell, M., Li, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

PubMed: 39088616 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.adk5901
Primary Citation of 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: 280.66 kDa
Atom Count: 19,167
Modeled Residue Count: 2,387
Deposited Residue Count: 2,407
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 4	A [auth 4]	319	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC4
UniProt
Find proteins for P40339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40339 Go to UniProtKB: P40339
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40339
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 3	B [auth 3]	327	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC3
UniProt
Find proteins for P38629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38629 Go to UniProtKB: P38629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38629
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 2	C [auth 2]	340	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC2
UniProt
Find proteins for P40348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40348 Go to UniProtKB: P40348
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40348
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 5	D [auth 5]	354	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC5
UniProt
Find proteins for P38251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38251 Go to UniProtKB: P38251
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38251
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome transmission fidelity protein 18	E [auth 1]	258	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CTF18
UniProt
Find proteins for P49956 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49956 Go to UniProtKB: P49956
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49956
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	F [auth A], G [auth B], H [auth C]	258	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: POL30, YBR088C, YBR0811
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15873 Go to UniProtKB: P15873
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15873
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 7
Molecule	Chains	Length	Organism	Image
Template DNA	I [auth T]	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 8
Molecule	Chains	Length	Organism	Image
Primer DNA	J [auth P]	17	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download Ideal Coordinates CCD File SDF format, chain K [auth 4] SDF format, chain M [auth 3] SDF format, chain O [auth 2] MOL2 format, chain K [auth 4] MOL2 format, chain M [auth 3] MOL2 format, chain O [auth 2] mmCIF format, chain K [auth 4] mmCIF format, chain M [auth 3] mmCIF format, chain O [auth 2]	K [auth 4], M [auth 3], O [auth 2]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain K [auth 4] Focus chain M [auth 3] Focus chain O [auth 2] Interactions & Density Focus chain K [auth 4] Focus chain M [auth 3] Focus chain O [auth 2]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain Q [auth 5] MOL2 format, chain Q [auth 5] mmCIF format, chain Q [auth 5]	Q [auth 5]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Q [auth 5] Interactions & Density Focus chain Q [auth 5]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth 4] SDF format, chain P [auth 2] SDF format, chain N [auth 3] MOL2 format, chain L [auth 4] MOL2 format, chain P [auth 2] MOL2 format, chain N [auth 3] mmCIF format, chain L [auth 4] mmCIF format, chain P [auth 2] mmCIF format, chain N [auth 3]	L [auth 4], N [auth 3], P [auth 2]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth 4] Focus chain N [auth 3] Focus chain P [auth 2] Interactions & Density Focus chain L [auth 4] Focus chain N [auth 3] Focus chain P [auth 2]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM131754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115809
Howard Hughes Medical Institute (HHMI)	United States	M.E.O.