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- EMDB-53485: Cryo-EM structure of rat SLCO2A1 bound to dinoprost. -

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Basic information

Entry
Database: EMDB / ID: EMD-53485
TitleCryo-EM structure of rat SLCO2A1 bound to dinoprost.
Map data
Sample
  • Complex: SLCO2A1 protein in detergent-lipid micelle bound to prostaglandin F2alpha, dinoprost.
    • Protein or peptide: Solute carrier organic anion transporter family member 2A1
  • Ligand: (Z)-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(E,3S)-3-oxidanyloct-1-enyl]cyclopentyl]hept-5-enoic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsOATP2A1 / plasma membrane localized / prostaglandin transporter / PGT / major facilitator superfamily. / MEMBRANE PROTEIN
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
Solute carrier organic anion transporter family member 2A1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDeme JC / Joshi C / Lea SM / Newstead S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust215519/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Structural basis for prostaglandin and drug transport via SLCO2A1.
Authors: Joshi C / Deme JC / Nakamura Y / Hsu W-T / Goult J / Kato T / Parker JL / Biggin PC / Lea SM / Nakanishi T / Newstead S
History
DepositionApr 24, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53485.png

Downloads & links

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Map

FileDownload / File: emd_53485.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 392 pix.
= 286.944 Å		0.73 Å/pix.
x 392 pix.
= 286.944 Å		0.73 Å/pix.
x 392 pix.
= 286.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.2305828 - 0.36914656
Average (Standard dev.)-0.00015997773 (±0.007728793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 286.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_53485_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53485_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53485_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SLCO2A1 protein in detergent-lipid micelle bound to prostaglandin...

EntireName: SLCO2A1 protein in detergent-lipid micelle bound to prostaglandin F2alpha, dinoprost.
Components
  • Complex: SLCO2A1 protein in detergent-lipid micelle bound to prostaglandin F2alpha, dinoprost.
    • Protein or peptide: Solute carrier organic anion transporter family member 2A1
  • Ligand: (Z)-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(E,3S)-3-oxidanyloct-1-enyl]cyclopentyl]hept-5-enoic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: SLCO2A1 protein in detergent-lipid micelle bound to prostaglandin...

SupramoleculeName: SLCO2A1 protein in detergent-lipid micelle bound to prostaglandin F2alpha, dinoprost.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Solute carrier organic anion transporter family member 2A1

MacromoleculeName: Solute carrier organic anion transporter family member 2A1
type: protein_or_peptide / ID: 1
Details: Fusion protein: Avi tag (GLNDIFEAQKIEWHE) Linker as restriction site used for cloning (XhoI): 3'-SLCO2A1-Avitag-LEGG-5'
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 72.615117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGLLLKPGAR QGSGTSSVPD RRCPRSVFSN IKVFVLCHGL LQLCQLLYSA YFKSSLTTIE KRFGLSSSSS GLISSLNEIS NATLIIFIS YFGSRVNRPR MIGIGGLLLA AGAFVLTLPH FLSEPYQYTS TTDGNRSSFQ TDLCQKHFGA LPPSKCHSTV P DTHKETSS ...String:
MGLLLKPGAR QGSGTSSVPD RRCPRSVFSN IKVFVLCHGL LQLCQLLYSA YFKSSLTTIE KRFGLSSSSS GLISSLNEIS NATLIIFIS YFGSRVNRPR MIGIGGLLLA AGAFVLTLPH FLSEPYQYTS TTDGNRSSFQ TDLCQKHFGA LPPSKCHSTV P DTHKETSS LWGLMVVAQL LAGIGTVPIQ PFGISYVDDF AEPTNSPLYI SILFAIAVFG PAFGYLLGSV MLRIFVDYGR VD TATVNLS PGDPRWIGAW WLGLLISSGF LIVTSLPFFF FPRAMSRGAE RSVTAEETMQ TEEDKSRGSL MDFIKRFPRI FLR LLMNPL FMLVVLSQCT FSSVIAGLST FLNKFLEKQY GATAAYANFL IGAVNLPAAA LGMLFGGILM KRFVFPLQTI PRVA ATIIT ISMILCVPLF FMGCSTSAVA EVYPPSTSSS IHPQQPPACR RDCSCPDSFF HPVCGDNGVE YVSPCHAGCS STNTS SEAS KEPIYLNCSC VSGGSASAKT GSCPTSCAQL LLPSIFLISF AALIACISHN PLYMMVLRVV NQDEKSFAIG VQFLLM RLL AWLPAPSLYG LLIDSSCVRW NYLCSGRRGA CAYYDNDALR NRYLGLQMVY KALGTLLLFF ISWRMKKNRE YSLQENT SG LIGLNDIFEA QKIEWHELEG G

UniProtKB: Solute carrier organic anion transporter family member 2A1

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Macromolecule #2: (Z)-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(E,3S)-3-oxidanyloct-1-...

MacromoleculeName: (Z)-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(E,3S)-3-oxidanyloct-1-enyl]cyclopentyl]hept-5-enoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: UGU
Molecular weightTheoretical: 354.481 Da
Chemical component information

ChemComp-UGU:
(Z)-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(E,3S)-3-oxidanyloct-1-enyl]cyclopentyl]hept-5-enoic acid / hormone*YM

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 61.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9949417
CTF correctionSoftware - Name: SIMPLE (ver. 3.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 206784
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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