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- EMDB-63867: Cryo-EM structure of human OAT4 in complex with DHEAS -

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Basic information

Entry
Database: EMDB / ID: EMD-63867
TitleCryo-EM structure of human OAT4 in complex with DHEAS
Map data
Sample
  • Complex: OAT4
    • Protein or peptide: Solute carrier family 22 member 11
  • Ligand: 17-oxoandrost-5-en-3beta-yl hydrogen sulfate
Keywordstransporter / OAT4 / organic anion transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Organic anion transport / sodium-independent organic anion transmembrane transporter activity / prostaglandin transport / prostaglandin transmembrane transporter activity / urate metabolic process / organic anion transport / solute:inorganic anion antiporter activity / organic anion transmembrane transporter activity / monoatomic ion transport / basal plasma membrane ...Organic anion transport / sodium-independent organic anion transmembrane transporter activity / prostaglandin transport / prostaglandin transmembrane transporter activity / urate metabolic process / organic anion transport / solute:inorganic anion antiporter activity / organic anion transmembrane transporter activity / monoatomic ion transport / basal plasma membrane / apical plasma membrane / external side of plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
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 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsZhang W / Chu Y / 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 OAT4 in complex with DHEAS
Authors: Zhang W / Chu Y / Zhang Y
History
DepositionMar 21, 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_63867.png

Downloads & links

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Map

FileDownload / File: emd_63867.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: 0.2
Minimum - Maximum-3.0952108 - 4.067159
Average (Standard dev.)0.0010341194 (±0.08983304)
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_63867_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_63867_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 : OAT4

EntireName: OAT4
Components
  • Complex: OAT4
    • Protein or peptide: Solute carrier family 22 member 11
  • Ligand: 17-oxoandrost-5-en-3beta-yl hydrogen sulfate

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Supramolecule #1: OAT4

SupramoleculeName: OAT4 / 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 11

MacromoleculeName: Solute carrier family 22 member 11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.769094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFSKLLEQA GGVGLFQTLQ VLTFILPCLM IPSQMLLENF SAAIPGHRCW THMLDNGSAV STNMTPKALL TISIPPGPNQ GPHQCRRFR QPQWQLLDPN ATATSWSEAD TEPCVDGWVY DRSVFTSTIV AKWDLVCSSQ GLKPLSQSIF MSGILVGSFI W GLLSYRFG ...String:
MAFSKLLEQA GGVGLFQTLQ VLTFILPCLM IPSQMLLENF SAAIPGHRCW THMLDNGSAV STNMTPKALL TISIPPGPNQ GPHQCRRFR QPQWQLLDPN ATATSWSEAD TEPCVDGWVY DRSVFTSTIV AKWDLVCSSQ GLKPLSQSIF MSGILVGSFI W GLLSYRFG RKPMLSWCCL QLAVAGTSTI FAPTFVIYCG LRFVAAFGMA GIFLSSLTLM VEWTTTSRRA VTMTVVGCAF SA GQAALGG LAFALRDWRT LQLAASVPFF AISLISWWLP ESARWLIIKG KPDQALQELR KVARINGHKE AKNLTIEVLM SSV KEEVAS AKEPRSVLDL FCVPVLRWRS CAMLVVNFSL LISYYGLVFD LQSLGRDIFL LQALFGAVDF LGRATTALLL SFLG RRTIQ AGSQAMAGLA ILANMLVPQD LQTLRVVFAV LGKGCFGISL TCLTIYKAEL FPTPVRMTAD GILHTVGRLG AMMGP LILM SRQALPLLPP LLYGVISIAS SLVVLFFLPE TQGLPLPDTI QDLESQKSTA AQGNRQEAVT VESTSLHHHH HHHHHH GSV EDYKDDDDK

UniProtKB: Solute carrier family 22 member 11

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Macromolecule #2: 17-oxoandrost-5-en-3beta-yl hydrogen sulfate

MacromoleculeName: 17-oxoandrost-5-en-3beta-yl hydrogen sulfate / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZWY
Molecular weightTheoretical: 368.488 Da
Chemical component information

ChemComp-ZWY:
17-oxoandrost-5-en-3beta-yl hydrogen sulfate

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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

Concentration10 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
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: 46.0 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: FEI TITAN KRIOS AUTOGRID HOLDER / 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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 164999
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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