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- EMDB-61048: Cryo-EM structure of hOAT1 in complex with cidofovir -

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Basic information

Entry
Database: EMDB / ID: EMD-61048
TitleCryo-EM structure of hOAT1 in complex with cidofovir
Map data
Sample
  • Complex: Cryo-EM structure of hOAT1 in complex with cidofovir
    • Protein or peptide: Solute carrier family 22 member 6
  • Ligand: ({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid
Keywordstransporter / Organic Anion / uptake / renal pathophysiology / TRANSPORT PROTEIN
Function / homology
Function and homology information


renal tubular secretion / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / Organic anion transport by SLC22 transporters / sodium-independent organic anion transport / : / metanephric proximal tubule development / prostaglandin transport / prostaglandin transmembrane transporter activity / organic anion transport ...renal tubular secretion / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / Organic anion transport by SLC22 transporters / sodium-independent organic anion transport / : / metanephric proximal tubule development / prostaglandin transport / prostaglandin transmembrane transporter activity / organic anion transport / solute:inorganic anion antiporter activity / : / monoatomic anion transport / antiporter activity / chloride ion binding / 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: 3.15 Å
AuthorsYang DX / Luo YB / Wu XN
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
Other governmentZYYC21006
Other government2022YFC2303700
CitationJournal: To be published
Title: Structural basis for recognition of two different drugs by human OAT1
Authors: Wu XN / Luo YB / Feng SJ
History
DepositionAug 2, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61048.png

Downloads & links

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Map

FileDownload / File: emd_61048.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.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.066
Minimum - Maximum-0.4278632 - 0.6663233
Average (Standard dev.)-0.00040306075 (±0.01334405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61048_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_61048_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 : Cryo-EM structure of hOAT1 in complex with cidofovir

EntireName: Cryo-EM structure of hOAT1 in complex with cidofovir
Components
  • Complex: Cryo-EM structure of hOAT1 in complex with cidofovir
    • Protein or peptide: Solute carrier family 22 member 6
  • Ligand: ({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid

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Supramolecule #1: Cryo-EM structure of hOAT1 in complex with cidofovir

SupramoleculeName: Cryo-EM structure of hOAT1 in complex with cidofovir / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 22 member 6

MacromoleculeName: 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: 61.869027 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 TVQDLESRWA PTQKEAGIYP RKGKQTRQQQ EHQKYMVPLQ ASAQEK NGL

UniProtKB: Solute carrier family 22 member 6

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Macromolecule #2: ({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]...

MacromoleculeName: ({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: L8P
Molecular weightTheoretical: 279.187 Da
Chemical component information

ChemComp-L8P:
({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.79 µm / Nominal defocus min: 0.876 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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