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- EMDB-48261: Human prostaglandin transporter(OATP2A1) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48261
TitleHuman prostaglandin transporter(OATP2A1)
Map datafinal cryoEM map sharpened with a -100 B-factor and filter resolution of 4 angstrom.
Sample
  • Complex: human prostaglandin transporter OATP2A1
    • Protein or peptide: Solute carrier organic anion transporter family member 2A1
  • Ligand: Digitonin
KeywordsProstaglandin / OATP / transporter / MEMBRANE PROTEIN / TRANSPORT 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsYu P / Orlando MA / Orlando BJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: Structure and Post-Translational Modification of the Prostaglandin Transporter
Authors: Yu P / Orlando MA / Orlando BJ
History
DepositionDec 11, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48261.png

Downloads & links

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Map

FileDownload / File: emd_48261.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal cryoEM map sharpened with a -100 B-factor and filter resolution of 4 angstrom.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 320 pix.
= 283.52 Å		0.89 Å/pix.
x 320 pix.
= 283.52 Å		0.89 Å/pix.
x 320 pix.
= 283.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.886 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0198
Minimum - Maximum-0.055390585 - 0.07484857
Average (Standard dev.)0.00007038043 (±0.002322129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 283.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unfiltered final cryoEM map

Fileemd_48261_additional_1.map
Annotationunfiltered final cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_48261_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48261_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human prostaglandin transporter OATP2A1

EntireName: human prostaglandin transporter OATP2A1
Components
  • Complex: human prostaglandin transporter OATP2A1
    • Protein or peptide: Solute carrier organic anion transporter family member 2A1
  • Ligand: Digitonin

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Supramolecule #1: human prostaglandin transporter OATP2A1

SupramoleculeName: human prostaglandin transporter OATP2A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: purified detergent solubilized prostaglandin transporter
Source (natural)Organism: Homo sapiens (human) / Location in cell: plasma membrane
Molecular weightTheoretical: 74.5 KDa

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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: Twin strep tag and a TEV cleavage site at the N terminus of PGT.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.56357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKG GGSGGGSGGG SSAWSHPQFE KGGGSENLYF QGGSGMGLLP KLGASQGSDT STSRAGRCAR SVFGNIKVFV LCQGLLQLC QLLYSAYFKS SLTTIEKRFG LSSSSSGLIS SLNEISNAIL IIFVSYFGSR VHRPRLIGIG GLFLAAGAFI L TLPHFLSE ...String:
MWSHPQFEKG GGSGGGSGGG SSAWSHPQFE KGGGSENLYF QGGSGMGLLP KLGASQGSDT STSRAGRCAR SVFGNIKVFV LCQGLLQLC QLLYSAYFKS SLTTIEKRFG LSSSSSGLIS SLNEISNAIL IIFVSYFGSR VHRPRLIGIG GLFLAAGAFI L TLPHFLSE PYQYTLASTG NNSRLQAELC QKHWQDLPPS KCHSTTQNPQ KETSSMWGLM VVAQLLAGIG TVPIQPFGIS YV DDFSEPS NSPLYISILF AISVFGPAFG YLLGSVMLQI FVDYGRVNTA AVNLVPGDPR WIGAWWLGLL ISSALLVLTS FPF FFFPRA MPIGAKRAPA TADEARKLEE AKSRGSLVDF IKRFPCIFLR LLMNSLFVLV VLAQCTFSSV IAGLSTFLNK FLEK QYGTS AAYANFLIGA VNLPAAALGM LFGGILMKRF VFSLQAIPRI ATTIITISMI LCVPLFFMGC STPTVAEVYP PSTSS SIHP QSPACRRDCS CPDSIFHPVC GDNGIEYLSP CHAGCSNINM SSATSKQLIY LNCSCVTGGS ASAKTGSCPV PCAHFL LPA IFLISFVSLI ACISHNPLYM MVLRVVNQEE KSFAIGVQFL LMRLLAWLPS PALYGLTIDH SCIRWNSLCL GRRGACA YY DNDALRDRYL GLQMGYKALG MLLLCFISWR VKKNKEYNVQ KAAGLI

UniProtKB: Solute carrier organic anion transporter family member 2A1

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Macromolecule #2: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 2 / Number of copies: 2 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

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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

Concentration3.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
25.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
0.06 w/vC56H92O29digitonin

Details: 25mM HEPES pH8.0, 150mM NaCl,0.06% digitonin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: Glow discharge in a Pelco EasyGlow 45s at 15mA.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 9088 / Average electron dose: 44.48 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsThe images were corrected for beam induced motion using patch motion correction in cryoSPARC.
Particle selectionNumber selected: 1795004
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Software - details: Patch CTF estimation / Details: Patch CTF estimation was performed in cryoSPARC. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Ab-initio reconstruction were used to generate the initial model.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 45842
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 50000 / Software - Name: RELION (ver. 5.0)
Details: The last round of the non-alignment 3D classification was performed using a mask around protein and blush regularization.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Chain ID: A / Chain - Residue range: 1-643 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsRefinement in phenix.real_space_refine
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9mgk:
Human prostaglandin transporter(OATP2A1)

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