9GY7 | pdb_00009gy7

C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP

PDB DOI: https://doi.org/10.2210/pdb9GY7/pdb
NAKB: 9GY7
EM Map EMD-51691: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Acetivibrio thermocellus, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-01 Released: 2025-12-24
Deposition Author(s): Nirwal, S., Czarnocki-Cieciura, M., Nowotny, M.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA.

Nirwal, S., Czarnocki-Cieciura, M., Zajko, W., Skowronek, K., Szczepanowski, R.H., Nowotny, M.

(2025) Nat Commun 17: 387-387

PubMed: 41381534 Search on PubMed
DOI: https://doi.org/10.1038/s41467-025-67075-y
Primary Citation Related Structures:
9GXK, 9GXL, 9GXM, 9GXN, 9GXO, 9GXP, 9GXQ, 9GXR, 9GXS, 9GXT, 9GXU, 9GXV, 9GXW, 9GY7

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 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.

Organizational Affiliation

Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.

Macromolecule Content

Total Structure Weight: 398.72 kDa
Atom Count: 21,176
Modeled Residue Count: 2,726
Deposited Residue Count: 3,346
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein A	A, B	962	Acetivibrio thermocellus	Mutation(s): 0 Gene Names: uvrA, Cthe_0311
UniProt
Find proteins for A3DC70 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DC70 Go to UniProtKB: A3DC70
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3DC70
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein B	E, F	661	Acetivibrio thermocellus	Mutation(s): 0 Gene Names: uvrB, Cthe_0309
UniProt
Find proteins for A3DC68 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DC68 Go to UniProtKB: A3DC68
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3DC68
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (50-MER) with a fluorescein modification - (random sequence built in model)	C, D	50	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], L [auth B], M [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]