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	Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA.
Journal, issue, pages	Nat Commun, Vol. 17, Issue 1, Page 387, Year 2025
Publish date	Dec 11, 2025
Authors	Shivlee Nirwal / Mariusz Czarnocki-Cieciura / Weronika Zajko / Krzysztof Skowronek / Roman H Szczepanowski / Marcin Nowotny /
PubMed Abstract	Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two ...Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two adenosine triphosphatase modules and forms dimers. The DNA is handed over from UvrA to UvrB, which is a weak helicase that verifies the presence of damage. Despite intense studies, the role of the ATPase activity of UvrA in damage recognition is unclear. Here, we present a series of cryo-electron microscopy structures of UvrA in complex with three different DNAs and in the presence and absence of nucleotides. We also present a structure of UvrA:UvrB:DNA complex. These structures reveal a major rearrangement of the UvrA dimer upon ATP binding. We propose that these conformational changes are used to mechanically probe the integrity of DNA for damage localization. Collectively, our results present snapshots of UvrA's ATP-dependent DNA damage detection.
External links	Nat Commun / PubMed:41381534 / PubMed Central
Methods	EM (single particle)
Resolution	2.74 - 4.81 Å
Structure data	51665 9gxk EMDB-51665, PDB-9gxk: C. thermocellum UvrA (basal conformation) Method: EM (single particle) / Resolution: 2.97 Å 51666 9gxl EMDB-51666, PDB-9gxl: C. thermocellum UvrA in complex with AMPPNP (basal conformation) Method: EM (single particle) / Resolution: 2.96 Å 51667 9gxm EMDB-51667, PDB-9gxm: C. thermocellum UvrA in complex with unmodified DNA and AMPPNP (basal conformation) Method: EM (single particle) / Resolution: 3.23 Å 51668 9gxn EMDB-51668, PDB-9gxn: C. thermocellum UvrA in complex with unmodified DNA and AMPPNP (ATP-bound conformation 1) Method: EM (single particle) / Resolution: 3.14 Å 51669 9gxo EMDB-51669, PDB-9gxo: C. thermocellum UvrA in complex with unmodified DNA and AMPPNP (ATP-bound conformation 2) Method: EM (single particle) / Resolution: 3.1 Å 51670 9gxp EMDB-51670, PDB-9gxp: C. thermocellum UvrA in complex with DNA with an abasic site (basal conformation) Method: EM (single particle) / Resolution: 3.84 Å 51671 9gxq EMDB-51671, PDB-9gxq: C. thermocellum UvrA in complex with DNA with an abasic site and AMPPNP (ATP-bound conformation 1) Method: EM (single particle) / Resolution: 2.74 Å 51672 9gxr EMDB-51672, PDB-9gxr: C. thermocellum UvrA in complex with DNA with an abasic site and AMPPNP (ATP-bound conformation 2) Method: EM (single particle) / Resolution: 3.04 Å 51673 9gxs EMDB-51673, PDB-9gxs: C. thermocellum UvrA in complex with DNA with a fluorescein modification (basal conformation) Method: EM (single particle) / Resolution: 3.14 Å 51674 9gxt EMDB-51674, PDB-9gxt: C. thermocellum UvrA in complex with DNA with a fluorescein modification and AMPPNP (ATP-bound conformation 1) Method: EM (single particle) / Resolution: 3.1 Å 51675 9gxu EMDB-51675, PDB-9gxu: C. thermocellum UvrA (K647A) in complex with DNA with a fluorescein modification (basal conformation) Method: EM (single particle) / Resolution: 4.81 Å 51676 9gxv EMDB-51676, PDB-9gxv: C. thermocellum UvrA in complex with DNA with a fluorescein modification and ADP (basal conformation) Method: EM (single particle) / Resolution: 3.87 Å EMDB-51677: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP: consensus map Method: EM (single particle) / Resolution: 2.97 Å 51678 9gxw EMDB-51678, PDB-9gxw: C. thermocellum UvrA (K39A) in complex with DNA with a fluorescein modification and AMPPNP (basal conformation) Method: EM (single particle) / Resolution: 3.63 Å EMDB-51690: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP: focused map Method: EM (single particle) / Resolution: 3.18 Å 51691 9gy7 EMDB-51691: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP (composite map) PDB-9gy7: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP Method: EM (single particle) / Resolution: 3.18 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM
Source	acetivibrio thermocellus (bacteria) synthetic construct (others)
Keywords	DNA BINDING PROTEIN / DNA Repair pathway / Nucleotide excision repair pathway / NER