Crystal structure of UvrA

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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Structure and mechanism of the UvrA-UvrB DNA damage sensor.

Pakotiprapha, D.Samuels, M.Shen, K.Hu, J.H.Jeruzalmi, D.

(2012) Nat Struct Mol Biol 19: 291-298

  • DOI: https://doi.org/10.1038/nsmb.2240
  • Primary Citation of Related Structures:  
    3UWX, 3UX8

  • PubMed Abstract: 

    Nucleotide excision repair (NER) is used by all organisms to eliminate DNA lesions. We determined the structure of the Geobacillus stearothermophilus UvrA-UvrB complex, the damage-sensor in bacterial NER and a new structure of UvrA. We observe that the DNA binding surface of UvrA, previously found in an open shape that binds damaged DNA, also exists in a closed groove shape compatible with native DNA only. The sensor contains two UvrB molecules that flank the UvrA dimer along the predicted path for DNA, ~80 Å from the lesion. We show that the conserved signature domain II of UvrA mediates a nexus of contacts among UvrA, UvrB and DNA. Further, in our new structure of UvrA, this domain adopts an altered conformation while an adjacent nucleotide binding site is vacant. Our findings raise unanticipated questions about NER and also suggest a revised picture of its early stages.

  • Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Excinuclease ABC, A subunit670Geobacillus sp. Y412MC52Mutation(s): 0 
Gene Names: GYMC52_3203uvrA
Find proteins for A0A0E0TG05 (Geobacillus sp. (strain Y412MC52))
Explore A0A0E0TG05 
Go to UniProtKB:  A0A0E0TG05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E0TG05
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.653α = 90
b = 51.33β = 97.27
c = 112.395γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Database references
  • Version 1.2: 2014-05-07
    Changes: Other
  • Version 1.3: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations