9PDQ | pdb_00009pdq

Human OCTN2 bound to carnitine in the occluded conformation

• PDB DOI: https://doi.org/10.2210/pdb9PDQ/pdb
• EM Map EMD-71540: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-06-30 Released: 2025-12-03 
• Deposition Author(s): Davies, J.S., Zeng, Y.Z., Stewart, A.G.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structural basis of sodium ion-dependent carnitine transport by OCTN2.

Davies, J.S., Zeng, Y.C., Briot, C., Brown, S.H.J., Ryan, R.M., Stewart, A.G.

(2025) Nat Commun 

• PubMed: 41318751 
• DOI: https://doi.org/10.1038/s41467-025-66867-6
• Primary Citation of Related Structures:  
  9PDQ, 9PFB, 9PMD


• PubMed Abstract: 
  

  Carnitine is essential for the import of long-chain fatty acids into mitochondria, where they are used for energy production. The carnitine transporter OCTN2 (novel organic cation transporter 2, SLC22A5) mediates carnitine uptake across the plasma membrane and as such facilitates fatty acid metabolism in most tissues. OCTN2 dysfunction causes systemic primary carnitine deficiency (SPCD), a potentially lethal disorder. Despite its importance in metabolism, the mechanism of high-affinity, sodium ion-dependent transport by OCTN2 is unclear. Here we report cryo-EM structures of human OCTN2 in three conformations: inward-facing ligand-free, occluded carnitine- and Na ⁺ -bound, and inward-facing ipratropium-bound. These structures define key interactions responsible for carnitine transport and identify an allosterically coupled Na ⁺ binding site housed within an aqueous cavity, separate from the carnitine-binding site. Combined with electrophysiology data, we provide a framework for understanding variants associated with SPCD and insight into how OCTN2 functions as the primary human carnitine transporter.

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Organizational Affiliation: 
• Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia. [e-mail].
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia. [e-mail].
School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW, Australia.
Molecular Horizons and School of Science, University of Wollongong, Wollongong, NSW, Australia.
School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia. [e-mail].
School of Biomedical Engineering, Faculty of Engineering, University of Sydney, Sydney, NSW, Australia. [e-mail].
Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia. [e-mail].
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 65.1 kDa 
• Atom Count: 4,267 
• Modeled Residue Count: 530 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Organic cation/carnitine transporter 2	A	570	Homo sapiens	Mutation(s): 0  Gene Names: SLC22A5, OCTN2
UniProt & NIH Common Fund Data Resources
Find proteins for O76082 (Homo sapiens) Explore O76082  Go to UniProtKB:  O76082
PHAROS:  O76082 GTEx:  ENSG00000197375
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: O76082-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
152 (Subject of Investigation/LOI)	C [auth A]	CARNITINE C7 H16 N O3 PHIQHXFUZVPYII-ZCFIWIBFSA-O
NA (Subject of Investigation/LOI)	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Davies, J.S., Zeng, Y.Z., Stewart, A.G.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP2016308

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Data collection, Database references