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- PDB-9r0n: Cryo-EM structure of rat SLCO2A1 bound to dinoprost. -

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Basic information

Entry
Database: PDB / ID: 9r0n
TitleCryo-EM structure of rat SLCO2A1 bound to dinoprost.
ComponentsSolute carrier organic anion transporter family member 2A1
KeywordsMEMBRANE PROTEIN / OATP2A1 / plasma membrane localized / prostaglandin transporter / PGT / major facilitator superfamily.
Function / homology
Function and homology information


Organic anion transport by SLCO transporters / sodium-independent organic anion transport / : / prostaglandin transport / prostaglandin transmembrane transporter activity / basal plasma membrane / basolateral plasma membrane / lysosome
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
Chem-UGU / CHOLESTEROL HEMISUCCINATE / Solute carrier organic anion transporter family member 2A1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDeme, J.C. / Joshi, C. / Lea, S.M. / Newstead, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust215519/Z/19/Z United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for prostaglandin and drug transport via SLCO2A1.
Authors: Chitra Joshi / Justin C Deme / Yoshinobu Nakamura / Wei-Tse Hsu / Jonathan D Goult / Takafumi Kato / Joanne L Parker / Philip C Biggin / Susan M Lea / Takeo Nakanishi / Simon Newstead /
Abstract: Organic anion-transporting polypeptide transporters (SLCO/OATPs) function as cellular gatekeepers, regulating intestinal absorption, hepatic and renal clearance, and the tissue distribution of drugs ...Organic anion-transporting polypeptide transporters (SLCO/OATPs) function as cellular gatekeepers, regulating intestinal absorption, hepatic and renal clearance, and the tissue distribution of drugs and metabolites in the human body. However, the mechanisms underlying substrate selection within the SLCO superfamily remain unclear, hampering efforts to rationalize the interaction of drugs and metabolites with these transporters. SLCO2A1 (also known as OATP2A1) is responsible for the distribution of eicosanoids, including prostaglandins (PGs) and thromboxanes, throughout the body, in addition to several families of nonsteroidal anti-inflammatory drugs (NSAIDs). Here, we present cryogenic electron microscopy structures of SLCO2A1 bound to endogenous PGs and to four widely prescribed medications for treating inflammation, chronic asthma, and Parkinson's disease (PD). Complementary molecular dynamics and in vivo cellular assays elucidate the molecular basis for PG and drug recognition. Our study reports essential mechanistic details that underpin substrate selection and subfamily adaptation within the broader SLCO superfamily of drug and metabolite transporters.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: 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)73,4563
Polymers72,6151
Non-polymers8412
Water00
1


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

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Components

#1: Protein Solute carrier organic anion transporter family member 2A1 / SLCO2A1 / Matrin F/G 1 / OATP2A1 / PHOAR2 / Prostaglandin transporter / PGT / Solute carrier family ...SLCO2A1 / Matrin F/G 1 / OATP2A1 / PHOAR2 / Prostaglandin transporter / PGT / Solute carrier family 21 member 2 / SLC21A2


Mass: 72615.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion protein: Avi tag (GLNDIFEAQKIEWHE) Linker as restriction site used for cloning (XhoI): 3'-SLCO2A1-Avitag-LEGG-5'
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slco2a1, Matr1, Slc21a2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q00910
#2: Chemical ChemComp-UGU / (Z)-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(E,3S)-3-oxidanyloct-1-enyl]cyclopentyl]hept-5-enoic acid / Dinoprost / Prostaglandin F2a / PGF2alpha


Mass: 354.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: SLCO2A1 protein in detergent-lipid micelle bound to prostaglandin F2alpha, dinoprost.
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F / Plasmid: pLEXm
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 61.2 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1SIMPLE3particle selection
4SIMPLE3CTF correction
9PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9949417
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 206784 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementHighest resolution: 3.4 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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