EMD-39354

Single-particle
5.15 Å
EMD-39354 Deposition: 03/03/2024
Map released: 04/12/2024
Last modified: 29/01/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-39354

Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D

EMD-39354

Single-particle
5.15 Å
EMD-39354 Deposition: 03/03/2024
Map released: 04/12/2024
Last modified: 29/01/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Homo sapiens
Sample: endogenous state D PCNA-DNA-FEN1-RNase H2 complex
Fitted models: 8yjz (Avg. Q-score: 0.302)

Deposition Authors: Tian Y , Gao N
Structural insight into Okazaki fragment maturation mediated by PCNA-bound FEN1 and RNaseH2.
Tian Y , Li N , Li Q , Gao N
(2025) EMBO J , 44 , 484 - 504
PUBMED: 39578540
DOI: doi:10.1038/s44318-024-00296-x
ISSN: 1460-2075
ASTM: EMJODG
Abstract:
PCNA is a master coordinator of many DNA-metabolic events. During DNA replication, the maturation of Okazaki fragments involves at least four DNA enzymes, all of which contain PCNA-interacting motifs. However, the temporal relationships and functional modulations between these PCNA-binding proteins are unclear. Here, we developed a strategy to purify endogenous PCNA-containing complexes from native chromatin, and characterized their structures using cryo-EM. Two structurally resolved classes (PCNA-FEN1 and PCNA-FEN1-RNaseH2 complexes) have captured a series of 3D snapshots for the primer-removal steps of Okazaki fragment maturation. These structures show that product release from FEN1 is a rate-liming step. Furthermore, both FEN1 and RNaseH2 undergo continuous conformational changes on PCNA that result in constant fluctuations in the bending angle of substrate DNA at the nick site, implying that these enzymes could regulate each other through conformational modulation of the bound DNA. The structures of the PCNA-FEN1-RNaseH2 complex confirm the toolbelt function of PCNA and suggests a potential unrecognized role of RNaseH2, as a dsDNA binding protein, in promoting the 5'-flap cleaving activity of FEN1.