7D5P

Structure of NorC transporter in an outward-open conformation in complex with a single-chain Indian camelid antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.298 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of inhibition of a transporter from Staphylococcus aureus, NorC, through a single-domain camelid antibody.

Kumar, S.Athreya, A.Gulati, A.Nair, R.M.Mahendran, I.Ranjan, R.Penmatsa, A.

(2021) Commun Biol 4: 836-836

  • DOI: https://doi.org/10.1038/s42003-021-02357-x
  • Primary Citation of Related Structures:  
    7D5P, 7D5Q

  • PubMed Abstract: 

    Transporters play vital roles in acquiring antimicrobial resistance among pathogenic bacteria. In this study, we report the X-ray structure of NorC, a 14-transmembrane major facilitator superfamily member that is implicated in fluoroquinolone resistance in drug-resistant Staphylococcus aureus strains, at a resolution of 3.6 Å. The NorC structure was determined in complex with a single-domain camelid antibody that interacts at the extracellular face of the transporter and stabilizes it in an outward-open conformation. The complementarity determining regions of the antibody enter and block solvent access to the interior of the vestibule, thereby inhibiting alternating-access. NorC specifically interacts with an organic cation, tetraphenylphosphonium, although it does not demonstrate an ability to transport it. The interaction is compromised in the presence of NorC-antibody complex, consequently establishing a strategy to detect and block NorC and related transporters through the use of single-domain camelid antibodies.


  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Drug transporter, putative
A, B
479Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: SACOL0086
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H2WZS4 (Staphylococcus aureus (strain COL))
Explore A0A0H2WZS4 
Go to UniProtKB:  A0A0H2WZS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2WZS4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ICab
C, D
131Camelus dromedariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.298 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.212α = 90
b = 139.875β = 106.03
c = 118.034γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
ADDREFdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustIndiaIA/1/15/2/502063
Department of Biotechnology (DBT, India)IndiaBT/PR31976/MED/29/1421/2019

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Refinement description, Structure summary