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- PDB-9wty: Structure of hOCTN1 in apo state -

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Basic information

Entry
Database: PDB / ID: 9wty
TitleStructure of hOCTN1 in apo state
ComponentsSolute carrier family 22 member 4
KeywordsMEMBRANE PROTEIN / transporter / cancer / drug target
Function / homology
Function and homology information


sulfur amino acid transport / carnitine transport / carnitine transmembrane transporter activity / acetylcholine uptake / quaternary ammonium group transmembrane transporter activity / amino-acid betaine transmembrane transporter activity / quaternary ammonium group transport / acetylcholine transmembrane transporter activity / Choline catabolism / amine transport ...sulfur amino acid transport / carnitine transport / carnitine transmembrane transporter activity / acetylcholine uptake / quaternary ammonium group transmembrane transporter activity / amino-acid betaine transmembrane transporter activity / quaternary ammonium group transport / acetylcholine transmembrane transporter activity / Choline catabolism / amine transport / SLC-mediated transport of organic cations / secondary active transmembrane transporter activity / sodium-independent organic anion transport / response to vitamin D / response to exogenous dsRNA / amino acid transmembrane transporter activity / xenobiotic transport / lactation / liver regeneration / amino acid import across plasma membrane / basal plasma membrane / PDZ domain binding / mitochondrial membrane / response to lipopolysaccharide / apical plasma membrane / neuronal cell body / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
Solute carrier family 22 members 4/5 / Organic cation transport protein/SVOP / Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 22 member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsXu, B.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2024YFA0916800 China
CitationJournal: Nat Commun / Year: 2026
Title: Structural and mechanistic insights into OCTN1-mediated transport and cancer cell proliferation
Authors: Xu, B. / Liang, S. / Wang, Z. / Zhou, X. / Wang, L. / Liang, Q. / Liu, X. / Guo, W. / Shi, S. / Zhu, C. / Ye, S. / Lou, Z. / Wang, Y.
History
DepositionSep 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 22 member 4


Theoretical massNumber of molelcules
Total (without water)62,2011
Polymers62,2011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier family 22 member 4 / Ergothioneine transporter / ET transporter / ETTh / Organic cation/carnitine transporter 1 / OCTN1


Mass: 62200.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC22A4, ETT, OCTN1, UT2H / Production host: Homo sapiens (human) / References: UniProt: Q9H015
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: hOCTN1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 348573 / Symmetry type: POINT
RefinementHighest resolution: 3.11 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044152
ELECTRON MICROSCOPYf_angle_d0.6375656
ELECTRON MICROSCOPYf_dihedral_angle_d4.205554
ELECTRON MICROSCOPYf_chiral_restr0.037654
ELECTRON MICROSCOPYf_plane_restr0.007699

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