8THD

Structure of the Saccharomyces cerevisiae clamp unloader Elg1-RFC bound to PCNA

PDB DOI: https://doi.org/10.2210/pdb8THD/pdb
EM Map EMD-41254: EMDB EMDataResource

Classification: REPLICATION
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2023-07-14 Released: 2024-05-22
Deposition Author(s): Zheng, F., Yao, Y.N., Georgescu, R., O'Donnell, M.E., 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: 3.25 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

Structure of the PCNA unloader Elg1-RFC.

Zheng, F., Yao, N.Y., Georgescu, R.E., Li, H., O'Donnell, M.E.

(2024) Sci Adv 10: eadl1739-eadl1739

PubMed: 38427736 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adl1739
Primary Citation of Related Structures:
8THB, 8THC, 8THD

PubMed Abstract:
During DNA replication, the proliferating cell nuclear antigen (PCNA) clamps are loaded onto primed sites for each Okazaki fragment synthesis by the AAA ⁺ heteropentamer replication factor C (RFC). PCNA encircling duplex DNA is quite stable and is removed from DNA by the dedicated clamp unloader Elg1-RFC. Here, we show the cryo-EM structure of Elg1-RFC in various states with PCNA. The structures reveal essential features of Elg1-RFC that explain how it is dedicated to PCNA unloading. Specifically, Elg1 contains two external loops that block opening of the Elg1-RFC complex for DNA binding, and an "Elg1 plug" domain that fills the central DNA binding chamber, thereby reinforcing the exclusive PCNA unloading activity of Elg1-RFC. Elg1-RFC was capable of unloading PCNA using non-hydrolyzable AMP-PNP. Both RFC and Elg1-RFC could remove PCNA from covalently closed circular DNA, indicating that PCNA unloading occurs by a mechanism that is distinct from PCNA loading. Implications for the PCNA unloading mechanism are discussed.

Organizational Affiliation

Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.

Macromolecule Content

Total Structure Weight: 335.12 kDa
Atom Count: 20,396
Modelled Residue Count: 2,553
Deposited Residue Count: 2,937
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELG1 isoform 1	A	791	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ELG1
UniProt
Find proteins for Q12050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12050 Go to UniProtKB: Q12050
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12050
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 4	B	323	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC4, YOL094C, O0923
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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 3	C	336	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC3, YNL290W, N0533
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

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 2	D	353	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC2, YJR068W, J1808
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

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 5	E	354	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC5, YBR087W, YBR0810
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

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	F, G, H	260	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PCNA
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

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 I [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D]	I [auth A], J [auth B], L [auth C], N [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain P [auth E] MOL2 format, chain P [auth E]	P [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain P [auth E] Interactions & Density Focus chain P [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D]	K [auth B], M [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-22

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	--