8THD

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

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 1.2 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

  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ELG1 isoform 1791Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ELG1
UniProt
Find proteins for Q12050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12050
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UniProt GroupQ12050
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 4323Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC4, YOL094C, O0923
UniProt
Find proteins for P40339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40339
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 3336Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC3, YNL290W, N0533
UniProt
Find proteins for P38629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38629
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 2353Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC2, YJR068W, J1808
UniProt
Find proteins for P40348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40348
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 5354Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC5, YBR087W, YBR0810
UniProt
Find proteins for P38251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38251
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen
F, G, H
260Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PCNA
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP15873
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS
Download Ideal Coordinates CCD File 
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
ADP
Query on ADP
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P [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
K [auth B],
M [auth C],
O [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data
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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Source and taxonomy, Structure summary