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- EMDB-37233: Molecular mechanism of prostaglandin transporter SLCO2A1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-37233
TitleMolecular mechanism of prostaglandin transporter SLCO2A1
Map data
Sample
  • Complex: Membrane Protein sample
    • Protein or peptide: Solute carrier organic anion transporter family member 2A1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSLCO family / 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 transmembrane transporter activity / sodium-independent organic anion transport / 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 transmembrane transporter activity / sodium-independent organic anion transport / 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: 3.2 Å
AuthorsLi YH / Qu QH / Zhu ZN / Chao YL / Zhou ZX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171194 China
CitationJournal: To Be Published
Title: Molecular mechanism of prostaglandin transporter SLCO2A1
Authors: Li YH / Qu QH
History
DepositionAug 19, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37233.png

Downloads & links

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Map

FileDownload / File: emd_37233.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 220 pix.
= 205.04 Å		0.93 Å/pix.
x 220 pix.
= 205.04 Å		0.93 Å/pix.
x 220 pix.
= 205.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.406
Minimum - Maximum-2.2760186 - 2.9433458
Average (Standard dev.)0.00044266292 (±0.07713949)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 205.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37233_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37233_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 : Membrane Protein sample

EntireName: Membrane Protein sample
Components
  • Complex: Membrane Protein sample
    • Protein or peptide: Solute carrier organic anion transporter family member 2A1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Membrane Protein sample

SupramoleculeName: Membrane Protein sample / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.543078 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-EGFP-MCS-pcDNA3.1 (others)
SequenceString: MGLLPKLGAS QGSDTSTSRA GRCARSVFGN IKVFVLCQGL LQLCQLLYSA YFKSSLTTIE KRFGLSSSSS GLISSLNEIS NAILIIFVS YFGSRVHRPR LIGIGGLFLA AGAFILTLPH FLSEPYQYTL ASTGNNSRLQ AELCQKHWQD LPPSKCHSTT Q NPQKETSS ...String:
MGLLPKLGAS QGSDTSTSRA GRCARSVFGN IKVFVLCQGL LQLCQLLYSA YFKSSLTTIE KRFGLSSSSS GLISSLNEIS NAILIIFVS YFGSRVHRPR LIGIGGLFLA AGAFILTLPH FLSEPYQYTL ASTGNNSRLQ AELCQKHWQD LPPSKCHSTT Q NPQKETSS MWGLMVVAQL LAGIGTVPIQ PFGISYVDDF SEPSNSPLYI SILFAISVFG PAFGYLLGSV MLQIFVDYGR VN TAAVNLV PGDPRWIGAW WLGLLISSAL LVLTSFPFFF FPRAMPIGAK RAPATADEAR KLEEAKSRGS LVDFIKRFPC IFL RLLMNS LFVLVVLAQC TFSSVIAGLS TFLNKFLEKQ YGTSAAYANF LIGAVNLPAA ALGMLFGGIL MKRFVFSLQA IPRI ATTII TISMILCVPL FFMGCSTPTV AEVYPPSTSS SIHPQSPACR RDCSCPDSIF HPVCGDNGIE YLSPCHAGCS NINMS SATS KQLIYLNCSC VTGGSASAKT GSCPVPCAHF LLPAIFLISF VSLIACISHN PLYMMVLRVV NQEEKSFAIG VQFLLM RLL AWLPSPALYG LTIDHSCIRW NSLCLGRRGA CAYYDNDALR DRYLGLQMGY KALGMLLLCF ISWRVK

UniProtKB: Solute carrier organic anion transporter family member 2A1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 238917
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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