[English] 日本語
Yorodumi
- PDB-9pdq: Human OCTN2 bound to carnitine in the occluded conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9pdq
TitleHuman OCTN2 bound to carnitine in the occluded conformation
ComponentsOrganic cation/carnitine transporter 2
KeywordsTRANSPORT PROTEIN / transporter / carnitine transporter / organic cation transporter / SLC22 family / sodium-dependent transport / membrane protein / solute carrier / metabolic transport / fatty acid oxidation / OCTN2 / SLC22A5
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
CARNITINE / Organic cation/carnitine transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsDavies, J.S. / Zeng, Y.Z. / Stewart, A.G.
Funding support Australia, 1items
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, J.S. / Zeng, Y.Z. / Stewart, A.G.
History
DepositionJun 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Organic cation/carnitine transporter 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1026
Polymers64,2531
Non-polymers8495
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Organic cation/carnitine transporter 2 / High-affinity sodium-dependent carnitine cotransporter / Solute carrier family 22 member 5


Mass: 64252.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC22A5, OCTN2 / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: O76082
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-152 / CARNITINE / (3-CARBOXY-2-(R)-HYDROXY-PROPYL)-TRIMETHYL-AMMONIUM


Mass: 162.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Novel organic cation transport 2 (OCTN2;SLC22A5) bound to carnitine in the occluded conformation.
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293-F / Plasmid: pEG BacMam
Buffer solutionpH: 8 / Details: Size-exclusion buffer containing 10 mM L-carnitine
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMSodium chlorideNaCl1
30.2 mMGlyco-diosgeninC56H92O251
410 mMCarnitineC7H15NO31
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was monodisperse after size-exclusion chromatography
Specimen supportDetails: Pelco EasyGlow 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 82 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
2EPU2.14image acquisition
7ISOLDE1.8model fitting
8Coot0.9.8.94model fitting
10cryoSPARC4.6initial Euler assignment
11cryoSPARC4.6final Euler assignment
12cryoSPARC4.6classification
13cryoSPARC4.63D reconstruction
14PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 6410000
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181269 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingAccession code: O76082 / Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 101.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034367
ELECTRON MICROSCOPYf_angle_d0.53945945
ELECTRON MICROSCOPYf_chiral_restr0.0391690
ELECTRON MICROSCOPYf_plane_restr0.0057733
ELECTRON MICROSCOPYf_dihedral_angle_d5.1003656

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more