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- PDB-9mgk: Human prostaglandin transporter(OATP2A1) -

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Basic information

Entry
Database: PDB / ID: 9mgk
TitleHuman prostaglandin transporter(OATP2A1)
ComponentsSolute carrier organic anion transporter family member 2A1
KeywordsTRANSPORT PROTEIN / Prostaglandin / OATP / transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLCO2A1 causes primary, autosomal recessive hypertrophic osteoarthropathy 2 (PHOAR2) / Transport of organic anions / sodium-independent organic anion transport / sodium-independent organic anion transmembrane transporter activity / prostaglandin transport / prostaglandin transmembrane transporter activity / lipid transporter activity / lipid transport / basal plasma membrane / basolateral plasma membrane ...Defective SLCO2A1 causes primary, autosomal recessive hypertrophic osteoarthropathy 2 (PHOAR2) / Transport of organic anions / sodium-independent organic anion transport / sodium-independent organic anion transmembrane transporter activity / prostaglandin transport / prostaglandin transmembrane transporter activity / lipid transporter activity / lipid transport / basal plasma membrane / basolateral plasma membrane / lysosome / membrane / plasma membrane
Similarity search - Function
Organic anion transporter polypeptide / Organic Anion Transporter Polypeptide (OATP) family / Kazal-type serine protease inhibitor domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier organic anion transporter family member 2A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsYu, P. / Orlando, M.A. / Orlando, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: Structure and Post-Translational Modification of the Prostaglandin Transporter
Authors: Yu, P. / Orlando, M.A. / Orlando, B.J.
History
DepositionDec 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / 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 organic anion transporter family member 2A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0223
Polymers74,5641
Non-polymers2,4592
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 organic anion transporter family member 2A1 / SLCO2A1 / OATP2A1 / PHOAR2 / Prostaglandin transporter / PGT / Solute carrier family 21 member 2 / SLC21A2


Mass: 74563.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Twin strep tag and a TEV cleavage site at the N terminus of PGT.
Source: (gene. exp.) Homo sapiens (human) / Gene: SLCO2A1, OATP2A1, SLC21A2 / Plasmid: pcDNA3.0 / Cell (production host): HEK293F / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q92959
#2: Chemical ChemComp-AJP / Digitonin


Mass: 1229.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C56H92O29 / Comment: detergent*YM
Has ligand of interestN
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: human prostaglandin transporter OATP2A1 / Type: COMPLEX
Details: purified detergent solubilized prostaglandin transporter
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.0745 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Cellular location: plasma membrane
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F / Plasmid: pCDNA3.0
Buffer solutionpH: 8 / Details: 25mM HEPES pH8.0, 150mM NaCl,0.06% digitonin
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
225 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
30.06 w/vdigitoninC56H92O291
SpecimenConc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Glow discharge in a Pelco EasyGlow 45s at 15mA. / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44.48 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9088

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.1particle selection
4cryoSPARC4.4.1CTF correctionPatch CTF estimation
7UCSF Chimera1.16model fitting
9cryoSPARC4.4.1initial Euler assignment
10RELION5final Euler assignment
11RELION5classification
12RELION53D reconstruction
13PHENIX1.21.1_5286model refinement
Image processingDetails: The images were corrected for beam induced motion using patch motion correction in cryoSPARC.
CTF correctionDetails: Patch CTF estimation was performed in cryoSPARC. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1795004
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45842 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: Refinement in phenix.real_space_refine
Atomic model buildingChain residue range: 1-643 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 4.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034248
ELECTRON MICROSCOPYf_angle_d0.6935798
ELECTRON MICROSCOPYf_dihedral_angle_d5.838801
ELECTRON MICROSCOPYf_chiral_restr0.046697
ELECTRON MICROSCOPYf_plane_restr0.005696

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