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- EMDB-71540: Human OCTN2 bound to carnitine in the occluded conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-71540
TitleHuman OCTN2 bound to carnitine in the occluded conformation
Map dataPrimary unsharpened map. Has strong density for the ligands of interest, carnitine and Na . Density for modelled water molecules require sharpened map (available as an auxiliary map).
Sample
  • Organelle or cellular component: Novel organic cation transport 2 (OCTN2;SLC22A5) bound to carnitine in the occluded conformation.
    • Protein or peptide: Organic cation/carnitine transporter 2
  • Ligand: SODIUM ION
  • Ligand: CARNITINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordstransporter / carnitine transporter / organic cation transporter / SLC22 family / sodium-dependent transport / membrane protein / solute carrier / metabolic transport / fatty acid oxidation / OCTN2 / SLC22A5 / TRANSPORT PROTEIN
Function / homology
Function and homology information


positive regulation of intestinal epithelial structure maintenance / sodium-dependent organic cation transport / (R)-carnitine transport / (R)-carnitine transmembrane transport / Defective SLC22A5 causes systemic primary carnitine deficiency (CDSP) / carnitine transport / carnitine transmembrane transport / carnitine transmembrane transporter activity / (R)-carnitine transmembrane transporter activity / quaternary ammonium group transmembrane transporter activity ...positive regulation of intestinal epithelial structure maintenance / sodium-dependent organic cation transport / (R)-carnitine transport / (R)-carnitine transmembrane transport / Defective SLC22A5 causes systemic primary carnitine deficiency (CDSP) / carnitine transport / carnitine transmembrane transport / carnitine transmembrane transporter activity / (R)-carnitine transmembrane transporter activity / quaternary ammonium group transmembrane transporter activity / amino-acid betaine transmembrane transporter activity / SLC-mediated transport of organic cations / quaternary ammonium group transport / response to symbiotic bacterium / Carnitine shuttle / symporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / sodium ion transport / response to tumor necrosis factor / xenobiotic transmembrane transporter activity / response to type II interferon / transport across blood-brain barrier / basal plasma membrane / PDZ domain binding / brush border membrane / apical plasma membrane / endoplasmic reticulum / extracellular exosome / ATP binding / plasma membrane / cytosol / cytoplasm
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
Organic cation/carnitine transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsDavies JS / Zeng YZ / Stewart AG
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2016308 Australia
CitationJournal: To Be Published
Title: Structural basis of sodium ion-dependent carnitine transport by OCTN2
Authors: Davies JS / Zeng YZ / Stewart AG
History
DepositionJun 30, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71540.png

Downloads & links

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Map

FileDownload / File: emd_71540.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary unsharpened map. Has strong density for the ligands of interest, carnitine and Na . Density for modelled water molecules require sharpened map (available as an auxiliary map).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0985
Minimum - Maximum-0.3151634 - 0.69132936
Average (Standard dev.)0.0000012076761 (±0.013128494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryosparc sharpened map (B-factor -75.5) that shows density...

Fileemd_71540_additional_1.map
AnnotationCryosparc sharpened map (B-factor -75.5) that shows density for modelled water molecules.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_71540_half_map_1.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_71540_half_map_2.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Novel organic cation transport 2 (OCTN2;SLC22A5) bound to carniti...

EntireName: Novel organic cation transport 2 (OCTN2;SLC22A5) bound to carnitine in the occluded conformation.
Components
  • Organelle or cellular component: Novel organic cation transport 2 (OCTN2;SLC22A5) bound to carnitine in the occluded conformation.
    • Protein or peptide: Organic cation/carnitine transporter 2
  • Ligand: SODIUM ION
  • Ligand: CARNITINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Novel organic cation transport 2 (OCTN2;SLC22A5) bound to carniti...

SupramoleculeName: Novel organic cation transport 2 (OCTN2;SLC22A5) bound to carnitine in the occluded conformation.
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Organic cation/carnitine transporter 2

MacromoleculeName: Organic cation/carnitine transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.252977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRDYDEVTAF LGEWGPFQRL IFFLLSASII PNGFTGLSSV FLIATPEHRC RVPDAANLSS AWRNHTVPLR LRDGREVPHS CRRYRLATI ANFSALGLEP GRDVDLGQLE QESCLDGWEF SQDVYLSTIV TEWNLVCEDD WKAPLTISLF FVGVLLGSFI S GQLSDRFG ...String:
MRDYDEVTAF LGEWGPFQRL IFFLLSASII PNGFTGLSSV FLIATPEHRC RVPDAANLSS AWRNHTVPLR LRDGREVPHS CRRYRLATI ANFSALGLEP GRDVDLGQLE QESCLDGWEF SQDVYLSTIV TEWNLVCEDD WKAPLTISLF FVGVLLGSFI S GQLSDRFG RKNVLFVTMG MQTGFSFLQI FSKNFEMFVV LFVLVGMGQI SNYVAAFVLG TEILGKSVRI IFSTLGVCIF YA FGYMVLP LFAYFIRDWR MLLVALTMPG VLCVALWWFI PESPRWLISQ GRFEEAEVII RKAAKANGIV VPSTIFDPSE LQD LSSKKQ QSHNILDLLR TWNIRMVTIM SIMLWMTISV GYFGLSLDTP NLHGDIFVNC FLSAMVEVPA YVLAWLLLQY LPRR YSMAT ALFLGGSVLL FMQLVPPDLY YLATVLVMVG KFGVTAAFSM VYVYTAELYP TVVRNMGVGV SSTASRLGSI LSPYF VYLG AYDRFLPYIL MGSLTILTAI LTLFLPESFG TPLPDTIDQM LRVKGMKHRK TPSHTRMLKD GQERPTILKS TAFGAA FES RLEVLFQ

UniProtKB: Organic cation/carnitine transporter 2

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: CARNITINE

MacromoleculeName: CARNITINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: 152
Molecular weightTheoretical: 162.207 Da
Chemical component information

ChemComp-152:
CARNITINE

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 11 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
0.2 mMC56H92O25Glyco-diosgenin
10.0 mMC7H15NO3Carnitine

Details: Size-exclusion buffer containing 10 mM L-carnitine
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: Pelco EasyGlow 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was monodisperse after size-exclusion chromatography

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 82.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6410000
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 181269
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6082


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9pdq:
Human OCTN2 bound to carnitine in the occluded conformation

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