7D5Q | pdb_00007d5q

Structure of NorC transporter (K398A mutant) in an outward-open conformation in complex with a single-chain Indian camelid antibody

• PDB DOI: https://doi.org/10.2210/pdb7D5Q/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus COL, Camelus dromedarius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2020-09-27 Released: 2021-06-09 
• Deposition Author(s): Kumar, S., Athreya, A., Penmatsa, A.
• Funding Organization(s): Wellcome Trust, Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 
  0.315 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.308 (Depositor), 0.310 (DCC) 
• R-Value Observed: 
  0.308 (Depositor) 

Starting Model: experimental

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

• PubMed: 34226658 
• DOI: https://doi.org/10.1038/s42003-021-02357-x
• Primary Citation 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.

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Organizational Affiliation: 
• Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
Van Andel Institute, Grand Rapids, MI, USA.
Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
Structural Parasitology Lab, International Centre for Genetic engineering and Biotechnology, New Delhi, India.
Principal Scientist, ICAR-National Research Centre of Camel (NRCC), Bikaner, India.
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.36 kDa 
• Atom Count: 7,489 
• Modeled Residue Count: 1,076 
• Deposited Residue Count: 1,220 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Drug transporter, putative	A, B	479	Staphylococcus aureus subsp. aureus COL	Mutation(s): 1  Gene Names: SACOL0086 Membrane Entity: Yes
UniProt
Find proteins for A0A0H2WZS4 (Staphylococcus aureus (strain COL)) Explore A0A0H2WZS4  Go to UniProtKB:  A0A0H2WZS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ICab	C, D	131	Camelus dromedarius	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth C], F [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free:  0.315 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.308 (Depositor), 0.310 (DCC) 
• R-Value Observed: 0.308 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.071	α = 90
b = 139.148	β = 105.66
c = 115.555	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Kumar, S., Athreya, A., Penmatsa, A.

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Funding Organization	Location	Grant Number
Wellcome Trust	India	IA/1/15/2/502063
Department of Biotechnology (DBT, India)	India	BT/PR31976/MED/29/1421/2019

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2021-07-14
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary