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.Z., Stewart, A.G.

To be published.

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