4Z3P | pdb_00004z3p

MATE transporter ClbM in complex with Rb+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.287 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

MATE transport of the E. coli-derived genotoxin colibactin.

Mousa, J.J.Yang, Y.Tomkovich, S.Shima, A.Newsome, R.C.Tripathi, P.Oswald, E.Bruner, S.D.Jobin, C.

(2016) Nat Microbiol 1: 15009-15009

  • DOI: https://doi.org/10.1038/nmicrobiol.2015.9
  • Primary Citation Related Structures: 
    4Z3N, 4Z3P

  • PubMed Abstract: 

    Various forms of cancer have been linked to the carcinogenic activities of microorganisms(1-3). The virulent gene island polyketide synthase (pks) produces the secondary metabolite colibactin, a genotoxic molecule(s) causing double-stranded DNA breaks(4) and enhanced colorectal cancer development(5,6). Colibactin biosynthesis involves a prodrug resistance strategy where an N-terminal prodrug scaffold (precolibactin) is assembled, transported into the periplasm and cleaved to release the mature product(7-10). Here, we show that ClbM, a multidrug and toxic compound extrusion (MATE) transporter, is a key component involved in colibactin activity and transport. Disruption of clbM attenuated pks+ E. coli-induced DNA damage in vitro and significantly decreased the DNA damage response in gnotobiotic Il10(-/-) mice. Colonization experiments performed in mice or zebrafish animal models indicate that clbM is not implicated in E. coli niche establishment. The X-ray structure of ClbM shows a structural motif common to the recently described MATE family. The 12-transmembrane ClbM is characterized as a cation-coupled antiporter, and residues important to the cation-binding site are identified. Our data identify ClbM as a precolibactin transporter and provide the first structure of a MATE transporter with a defined and specific biological function.


  • Organizational Affiliation
    • Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.

Macromolecule Content 

  • Total Structure Weight: 55.49 kDa 
  • Atom Count: 3,352 
  • Modeled Residue Count: 431 
  • Deposited Residue Count: 499 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative drug/sodium antiporter499Escherichia coliMutation(s): 0 
Gene Names: clbM
Membrane Entity: Yes 
UniProt
Find proteins for Q0P7K3 (Escherichia coli)
Explore Q0P7K3 
Go to UniProtKB:  Q0P7K3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0P7K3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.287 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.22α = 90
b = 80.22β = 90
c = 175.251γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description