Wild type GapR crystal structure 2 from C. crescentus

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report

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Structures of GapR reveal a central channel which could accommodate B-DNA.

Tarry, M.J.Harmel, C.Taylor, J.A.Marczynski, G.T.Schmeing, T.M.

(2019) Sci Rep 9: 16679-16679

  • DOI: https://doi.org/10.1038/s41598-019-52964-2
  • Primary Citation of Related Structures:  
    6OZX, 6OZY, 6OZZ

  • PubMed Abstract: 

    GapR is a nucleoid-associated protein required for the cell cycle of Caulobacter cresentus. We have determined new crystal structures of GapR to high resolution. As in a recently published structure, a GapR monomer folds into one long N-terminal α helix and two shorter α helices, and assembles into a tetrameric ring with a closed, positively charged, central channel. In contrast to the conclusions drawn from the published structures, we observe that the central channel of the tetramer presented here could freely accommodate B-DNA. Mutation of six conserved lysine residues lining the cavity and electrophoretic mobility gel shift experiments confirmed their role in DNA binding and the channel as the site of DNA binding. Although present in our crystals, DNA could not be observed in the electron density maps, suggesting that DNA binding is non-specific, which could be important for tetramer-ring translocation along the chromosome. In conjunction with previous GapR structures we propose a model for DNA binding and translocation that explains key published observations on GapR and its biological functions.

  • Organizational Affiliation

    Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC, H3A 2B4, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0335 protein CC_3319
A, B
113Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: CC_3319
Find proteins for Q9A385 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Explore Q9A385 
Go to UniProtKB:  Q9A385
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A385
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.77α = 90
b = 59.37β = 90
c = 93.94γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN-148472
Canadian Institutes of Health Research (CIHR)CanadaMOP-125998

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Data collection, Database references