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- EMDB-63862: Cryo-EM structure of human OAT1 in complex with probenecid -

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Basic information

Entry
Database: EMDB / ID: EMD-63862
TitleCryo-EM structure of human OAT1 in complex with probenecid
Map data
Sample
  • Complex: OAT1
    • Protein or peptide: Isoform 2 of Solute carrier family 22 member 6
  • Ligand: 4-(dipropylsulfamoyl)benzoic acid
Keywordstransporter / OAT1 / organic anion transport / MEMBRANE PROTEIN
Function / homology
Function and homology information


renal tubular secretion / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / sodium-independent organic anion transport / Organic anion transport / sodium-independent organic anion transmembrane transporter activity / metanephric proximal tubule development / prostaglandin transport / prostaglandin transmembrane transporter activity / organic anion transport ...renal tubular secretion / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / sodium-independent organic anion transport / Organic anion transport / sodium-independent organic anion transmembrane transporter activity / metanephric proximal tubule development / prostaglandin transport / prostaglandin transmembrane transporter activity / organic anion transport / solute:inorganic anion antiporter activity / organic anion transmembrane transporter activity / monoatomic anion transport / chloride ion binding / antiporter activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / basal plasma membrane / : / caveola / basolateral plasma membrane / protein-containing complex / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Organic cation transport protein/SVOP / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 22 member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsZhang W / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human OAT1 in complex with probenecid
Authors: Zhang W / Zhang Y
History
DepositionMar 20, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63862.png

Downloads & links

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Map

FileDownload / File: emd_63862.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 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: 0.2
Minimum - Maximum-1.9382117 - 2.9521723
Average (Standard dev.)-0.00062027806 (±0.060555566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63862_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_63862_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 : OAT1

EntireName: OAT1
Components
  • Complex: OAT1
    • Protein or peptide: Isoform 2 of Solute carrier family 22 member 6
  • Ligand: 4-(dipropylsulfamoyl)benzoic acid

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Supramolecule #1: OAT1

SupramoleculeName: OAT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Solute carrier family 22 member 6

MacromoleculeName: Isoform 2 of Solute carrier family 22 member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.119156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFNDLLQQV GGVGRFQQIQ VTLVVLPLLL MASHNTLQNF TAAIPTHHCR PPADANLSKN GGLEVWLPRD RQGQPESCLR FTSPQWGLP FLNGTEANGT GATEPCTDGW IYDNSTFPST IVTEWDLVCS HRALRQLAQS LYMVGVLLGA MVFGYLADRL G RRKVLILN ...String:
MAFNDLLQQV GGVGRFQQIQ VTLVVLPLLL MASHNTLQNF TAAIPTHHCR PPADANLSKN GGLEVWLPRD RQGQPESCLR FTSPQWGLP FLNGTEANGT GATEPCTDGW IYDNSTFPST IVTEWDLVCS HRALRQLAQS LYMVGVLLGA MVFGYLADRL G RRKVLILN YLQTAVSGTC AAFAPNFPIY CAFRLLSGMA LAGISLNCMT LNVEWMPIHT RACVGTLIGY VYSLGQFLLA GV AYAVPHW RHLQLLVSAP FFAFFIYSWF FIESARWHSS SGRLDLTLRA LQRVARINGK REEGAKLSME VLRASLQKEL TMG KGQASA MELLRCPTLR HLFLCLSMLW FATSFAYYGL VMDLQGFGVS IYLIQVIFGA VDLPAKLVGF LVINSLGRRP AQMA ALLLA GICILLNGVI PQDQSIVRTS LAVLGKGCLA ASFNCIFLYT GELYPTMIRQ TGMGMGSTMA RVGSIVSPLV SMTAE LYPS MPLFIYGAVP VAASAVTVLL PETLGQPLPD TVQDLESRKG KQTRQQQEHQ KYMVPLQASA QEKNGLHHHH HHHHHH GSV EDYKDDDDK

UniProtKB: Solute carrier family 22 member 6

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Macromolecule #2: 4-(dipropylsulfamoyl)benzoic acid

MacromoleculeName: 4-(dipropylsulfamoyl)benzoic acid / type: ligand / ID: 2 / Number of copies: 1 / Formula: RTO
Molecular weightTheoretical: 285.359 Da
Chemical component information

ChemComp-RTO:
4-(dipropylsulfamoyl)benzoic acid

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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

Concentration5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (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 / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FISCHIONE 2550 / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82328
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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