7TFI

Atomic model of the S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to DNA with an open clamp

Summary for 7TFI

• Entry DOI: 10.2210/pdb7tfi/pdb
• EMDB information: 25872 25873 25874 25875 25876
• Descriptor: Replication factor C subunit 1, MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE, ... (11 entities in total)
• Functional Keywords: dna replication, dna damage repair, rfc loader, pcna clamp, dna polymerase processivity factor, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 10
• Total formula weight: 358410.78

Authors

Zheng, F.,Georgescu, R.,Yao, Y.N.,O'Donnell, M.E.,Li, H. (deposition date: 2022-01-06, release date: 2022-11-16, Last modification date: 2025-05-21)

Primary citation

Zheng, F.,Georgescu, R.,Yao, N.Y.,Li, H.,O'Donnell, M.E.
Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair.
Elife, 11:-, 2022

PubMed Abstract: RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases δ and ε. The RFC pentamer forms a central chamber that binds 3' ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a second DNA binding site in RFC that binds a 5' duplex. This 5' DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3' and 5' ends are present at a ssDNA gap, we propose that the 5' site facilitates RFC's PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5' DNA binding domain of Rfc1. We further observe that a 5' end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5'-DNA site in lagging strand DNA synthesis.

PubMed: 35829698
DOI: 10.7554/eLife.77469

Experimental method

ELECTRON MICROSCOPY (3.41 Å)