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- PDB-9gxt: C. thermocellum UvrA in complex with DNA with a fluorescein modif... -

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Basic information

Entry
Database: PDB / ID: 9gxt
TitleC. thermocellum UvrA in complex with DNA with a fluorescein modification and AMPPNP (ATP-bound conformation 1)
Components
  • DNA (50-MER) with a fluorescein modification - (random sequence built in model)
  • UvrABC system protein A
KeywordsDNA BINDING PROTEIN / DNA Repair pathway / Nucleotide excision repair pathway / NER
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / UvrABC system protein A
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNirwal, S. / Czarnocki-Cieciura, M. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/A/NZ1/01098 Poland
CitationJournal: Nat Commun / Year: 2025
Title: Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA.
Authors: Shivlee Nirwal / Mariusz Czarnocki-Cieciura / Weronika Zajko / Krzysztof Skowronek / Roman H Szczepanowski / Marcin Nowotny /
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.
History
DepositionSep 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 2 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UvrABC system protein A
B: UvrABC system protein A
C: DNA (50-MER) with a fluorescein modification - (random sequence built in model)
D: DNA (50-MER) with a fluorescein modification - (random sequence built in model)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,26910
Polymers245,1134
Non-polymers2,1566
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein UvrABC system protein A / UvrA protein / Excinuclease ABC subunit A


Mass: 107144.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Gene: uvrA, Cthe_0311 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DC70
#2: DNA chain DNA (50-MER) with a fluorescein modification - (random sequence built in model)


Mass: 15411.887 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Random sequence built in model. / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: C. thermocellum UvrA in complex with DNA with a fluorescein modification and AMPPNP
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.247 MDa / Experimental value: NO
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample fixed with 0.01% glutaraldehyde and concentrated prior to vitrification; exact concentration cannot be estimated accurately.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 40.54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10348 / Details: 4860 images were collected with 30 deg stage tilt
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9.6particle selection
2EPU2.10.0.1941RELimage acquisition
4CTFFIND4.1.14CTF correction
10cryoSPARC4.5final Euler assignment
12cryoSPARC4.53D reconstruction
13PHENIX1.21.2-5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3577433
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126432 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 71.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002111390
ELECTRON MICROSCOPYf_angle_d0.506815744
ELECTRON MICROSCOPYf_chiral_restr0.03841828
ELECTRON MICROSCOPYf_plane_restr0.00251772
ELECTRON MICROSCOPYf_dihedral_angle_d17.62072258

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