9OYI

Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 1 with fully open clamp and unsettled DNA

Summary for 9OYI

• Entry DOI: 10.2210/pdb9oyi/pdb
• EMDB information: 71022
• Descriptor: DNA polymerase III subunit delta, MAGNESIUM ION, DNA polymerase III subunit tau, ... (10 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: 10
• Total formula weight: 409338.41

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, Last modification date: 2026-10-07)

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.
Mol.Cell, 86:2055-2069.e10, 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 single-stranded DNA (ssDNA) gaps-common DNA repair intermediates-remains unclear. Here, we show that the bacterial E. coli DnaX clamp loader uses a mechanism distinct from its eukaryotic counterpart. Whereas eukaryotic replication factor C (RFC) unwinds DNA at the recessed 3' end and stabilizes the 5'-dsDNA (double-stranded DNA) at a 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 contains a conserved external DNA-binding site that bends gapped DNA by ∼150°, promoting insertion of 3'-dsDNA into the clamp. This DNA-bending mechanism enables efficient β-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy likely important for DNA repair.

PubMed: 42140189
DOI: 10.1016/j.molcel.2026.04.020

Experimental method

ELECTRON MICROSCOPY (2.54 Å)