9GA4 | pdb_00009ga4

MtUvrA2UvrB2 bound to damaged oligonucleotide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanistic understanding of UvrA damage detection and lesion hand-off to UvrB in Nucleotide Excision Repair.

Genta, M.Ferrara, G.Capelli, R.Rondelli, D.Sertic, S.Bolognesi, M.Rizzi, M.Rossi, F.Jeruzalmi, D.Chaves-Sanjuan, A.Miggiano, R.

(2025) Nat Commun 16: 3416-3416

  • DOI: https://doi.org/10.1038/s41467-025-58670-0
  • Primary Citation of Related Structures:  
    9GA2, 9GA3, 9GA4, 9GA5

  • PubMed Abstract: 

    Nucleotide excision repair (NER) represents one of the major molecular machineries that control chromosome stability in all living species. In Eubacteria, the initial stages of the repair process are carried out by the UvrABC excinuclease complex. Despite the wealth of structural data available, some crucial details of the pathway remain elusive. In this study, we present a structural investigation of the Mycobacterium tuberculosis UvrAUvrB complex and of the UvrA dimer, both in complex with damaged DNA. Our analyses yield insights into the DNA binding mode of UvrA, showing an unexplored conformation of Insertion Domains (IDs), underlying the essential role of these domains in DNA coordination. Furthermore, we observe an interplay between the ID and the UvrB Binding Domain (UBD): after the recognition of the damage, the IDs repositions with the concomitant reorganization of UBD, allowing the formation of the complex between UvrA and UvrB. These events are detected along the formation of the uncharacterized UvrA 2 UvrB 1 -DNA and the UvrA 2 UvrB 2 -DNA complexes which we interpret as hierarchical steps initiating the DNA repair cascade in the NER pathway, resulting in the formation of the pre-incision complex.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100, Novara, Italy.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UvrABC system protein A
A, B
993Mycobacterium tuberculosisMutation(s): 0 
Gene Names: uvrARv1638MTCY06H11.02
UniProt
Find proteins for P9WQK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQK7 
Go to UniProtKB:  P9WQK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQK7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UvrABC system protein BC,
F [auth D]
720Mycobacterium tuberculosisMutation(s): 0 
Gene Names: uvrBRv1633MTCY01B2.25
UniProt
Find proteins for P9WFC7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFC7 
Go to UniProtKB:  P9WFC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFC7
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNAD [auth E],
E [auth F]
42Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItalyP2022P8KMF

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection