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- PDB-9u5a: Cryo-EM structure of human OAT4 in complex with DHEAS -

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Basic information

Entry
Database: PDB / ID: 9u5a
TitleCryo-EM structure of human OAT4 in complex with DHEAS
ComponentsSolute carrier family 22 member 11
KeywordsMEMBRANE PROTEIN / transporter / OAT4 / organic anion transporter
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
17-oxoandrost-5-en-3beta-yl hydrogen sulfate / Solute carrier family 22 member 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsZhang, W. / Chu, Y. / Zhang, Y.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 22 member 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1382
Polymers62,7691
Non-polymers3681
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Solute carrier family 22 member 11 / Organic anion transporter 4 / OAT4 / Organic anion:dicarboxylate exchanger OAT4


Mass: 62769.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC22A11, OAT4 / Production host: Homo sapiens (human) / References: UniProt: Q9NSA0
#2: Chemical ChemComp-ZWY / 17-oxoandrost-5-en-3beta-yl hydrogen sulfate / Dehydroepiandrosterone sulfate / DHEA sulfate / DHEA-S


Mass: 368.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: OAT4 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 900 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 46 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164999 / Symmetry type: POINT

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