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- EMDB-40948: RELION reconstruction of rat organic anion transporter 1 (OAT1) -

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Basic information

Entry
Database: EMDB / ID: EMD-40948
TitleRELION reconstruction of rat organic anion transporter 1 (OAT1)
Map data
Sample
  • Complex: Rat OAT1 solubilized in detergent LMNG
Keywordsorganic anion transporter / OAT / SLC22 / drug transporter / TRANSPORT PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.23 Å
AuthorsDou T / Jiang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: The substrate and inhibitor binding mechanism of polyspecific transporter OAT1 revealed by high-resolution cryo-EM.
Authors: Tongyi Dou / Tengfei Lian / Shi Shu / Yi He / Jiansen Jiang /
Abstract: Organic anion transporters (OATs) of the SLC22 family have crucial roles in the transport of organic anions, including metabolites and therapeutic drugs, and in transporter-mediated drug-drug ...Organic anion transporters (OATs) of the SLC22 family have crucial roles in the transport of organic anions, including metabolites and therapeutic drugs, and in transporter-mediated drug-drug interactions. In the kidneys, OATs facilitate the elimination of metabolic waste products and xenobiotics. However, their transport activities can lead to the accumulation of certain toxic compounds within cells, causing kidney damage. Moreover, OATs are important drug targets, because their inhibition modulates the elimination or retention of substrates linked to diseases. Despite extensive research on OATs, the molecular basis of their substrate and inhibitor binding remains poorly understood. Here we report the cryo-EM structures of rat OAT1 (also known as SLC22A6) and its complexes with para-aminohippuric acid and probenecid at 2.1, 2.8 and 2.9 Å resolution, respectively. Our findings reveal a highly conserved substrate binding mechanism for SLC22 transporters, wherein four aromatic residues form a cage to accommodate the polyspecific binding of diverse compounds.
History
DepositionJun 1, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40948.png

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Map

FileDownload / File: emd_40948.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 160 pix.
= 132.8 Å		0.83 Å/pix.
x 160 pix.
= 132.8 Å		0.83 Å/pix.
x 160 pix.
= 132.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.14294639 - 0.24333568
Average (Standard dev.)0.0001005983 (±0.010474044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 132.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40948_msk_1.map
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Half map: #1

Fileemd_40948_half_map_1.map
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Half map: #2

Fileemd_40948_half_map_2.map
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Sample components

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Entire : Rat OAT1 solubilized in detergent LMNG

EntireName: Rat OAT1 solubilized in detergent LMNG
Components
  • Complex: Rat OAT1 solubilized in detergent LMNG

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Supramolecule #1: Rat OAT1 solubilized in detergent LMNG

SupramoleculeName: Rat OAT1 solubilized in detergent LMNG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 61 KDa

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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: 8
Details: TBS buffer (20 mM Tris-HCl, 150 mM NaCl, pH 8.0) with 0.01% LMNG
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 8245 / Average exposure time: 6.25 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
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

Startup modelType of model: OTHER
Details: The initial model was generated using the ab-initio reconstruction in cryoSPARC2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 395953
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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