Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	The DnaX clamp loader sharply bends DNA to load β-clamp at nicks and small gaps.
Journal, issue, pages	bioRxiv, Year 2026
Publish date	Jan 20, 2026
Authors	Fengwei Zheng / Nina Y Yao / Roxana E Georgescu / Meinan Lyu / Michael E O'Donnell / Huilin Li /
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 ...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.
External links	bioRxiv / PubMed:41648351 / PubMed Central
Methods	EM (single particle)
Resolution	2.53 - 3.14 Å
Structure data	71013 9oyb EMDB-71013: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 1 with flexibly bound DNA at the shoulder PDB-9oyb: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 1 with flexibly bound DNA at the shoulder Method: EM (single particle) / Resolution: 3.14 Å 71014 9oyc EMDB-71014: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 2 with flexibly bound DNA at the shoulder PDB-9oyc: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 2 with flexibly bound DNA at the shoulder Method: EM (single particle) / Resolution: 2.71 Å 71015 9oyd EMDB-71015: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 3 with disordered DNA at the shoulder PDB-9oyd: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 3 with disordered DNA at the shoulder Method: EM (single particle) / Resolution: 2.73 Å 71016 9oye EMDB-71016: Cryo-EM map 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 PDB-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 Method: EM (single particle) / Resolution: 2.72 Å 71017 9oyf EMDB-71017: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 2 conformer 2 with less bent DNA PDB-9oyf: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 2 conformer 2 with less bent DNA Method: EM (single particle) / Resolution: 3.12 Å 71018 9oyg EMDB-71018: Cryo-EM map of the E. coli clamp loader DnaX-complex alone PDB-9oyg: Structure of the E. coli clamp loader DnaX-complex alone Method: EM (single particle) / Resolution: 2.95 Å 71021 9oyh EMDB-71021: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state PDB-9oyh: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state Method: EM (single particle) / Resolution: 2.54 Å 71022 9oyi EMDB-71022: Cryo-EM map 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 PDB-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 Method: EM (single particle) / Resolution: 2.54 Å 71023 9oyj EMDB-71023: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 2 with fully open clamp and settled DNA PDB-9oyj: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 2 with fully open clamp and settled DNA Method: EM (single particle) / Resolution: 2.53 Å 71024 9oyk EMDB-71024: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 3 with partially closed clamp PDB-9oyk: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 3 with partially closed clamp Method: EM (single particle) / Resolution: 2.6 Å 71025 9oyl EMDB-71025: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 4 with fully closed clamp PDB-9oyl: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 4 with fully closed clamp Method: EM (single particle) / Resolution: 2.88 Å 71026 9oym EMDB-71026: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 5 with fully closed clamp PDB-9oym: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 5 with fully closed clamp Method: EM (single particle) / Resolution: 2.6 Å 71027 9oyn EMDB-71027: Cryo-EM map of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 6 with fully closed clamp PDB-9oyn: Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 6 with fully closed clamp Method: EM (single particle) / Resolution: 2.7 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM
Source	escherichia coli (E. coli) dna molecule (others)
Keywords	REPLICATION/DNA / E. coli / DNA replication / DNA damage repair / clamp loading complex / clamp beta / clamp loader DnaX-complex / REPLICATION / REPLICATION-DNA complex / TRANSFERASE