9OYE

Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 2 conformer 1 with sharply bent DNA

Summary for 9OYE

• Entry DOI: 10.2210/pdb9oye/pdb
• EMDB information: 71016
• Descriptor: DNA polymerase III subunit delta, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, MAGNESIUM ION, ... (11 entities in total)
• Functional Keywords: dna replication, dna damage repair, clamp loading complex, clamp beta, clamp loader dnax-complex, replication, replication-dna complex, replication/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 11
• Total formula weight: 412653.61

Authors

Zheng, F.,Yao, Y.N.,Georgescu, R.,Lyu, M.,O'Donnell, M.E.,Li, H. (deposition date: 2025-06-04, release date: 2026-04-29)

Primary citation

Zheng, F.,Yao, N.Y.,Georgescu, R.E.,Lyu, M.,O'Donnell, M.E.,Li, H.
The E. coli DnaX clamp loader sharply bends DNA to load beta-clamp at nicks and small gaps.
Biorxiv, 2026

PubMed Abstract: DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks and small ssDNA gaps-common intermediates during DNA repair-remains incompletely understood. Here, we show that the bacterial DnaX clamp loader employs a fundamentally different mechanism from its eukaryotic counterpart. Whereas eukaryotic RFC unwinds DNA at the recessed 3' end and stabilizes the 5'-dsDNA at a dedicated shoulder site, the bacterial DnaX-complex neither unwinds DNA nor stably binds the 5'-dsDNA in vitro. Instead, cryo-EM structures reveal that the β-clamp itself contains a conserved external DNA-binding site that enables sharp bending of gapped DNA by ~150°, promoting insertion of the 3'-dsDNA into the clamp. This DNA-bending mechanism allows efficient β-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy for clamp loading. Because small DNA gaps are frequently associated with DNA damage, clamps loaded at these sites are likely important for DNA repair.

PubMed: 41648351
DOI: 10.64898/2026.01.17.700081

Experimental method

ELECTRON MICROSCOPY (2.72 Å)