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- PDB-9dxo: Cryo-EM structure of human OATP1C1 F240A mutant in complex with e... -

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Basic information

Entry
Database: PDB / ID: 9dxo
TitleCryo-EM structure of human OATP1C1 F240A mutant in complex with estrone 3-sulfate
ComponentsSolute carrier organic anion transporter family member 1C1
KeywordsTRANSPORT PROTEIN / SLC transporter / E1S
Function / homology
Function and homology information


positive regulation of thyroid hormone generation / Transport of organic anions / sodium-independent organic anion transport / sodium-independent organic anion transmembrane transporter activity / thyroid hormone transmembrane transporter activity / thyroid hormone transport / organic anion transmembrane transporter activity / bile acid transmembrane transporter activity / bile acid and bile salt transport / transport across blood-brain barrier ...positive regulation of thyroid hormone generation / Transport of organic anions / sodium-independent organic anion transport / sodium-independent organic anion transmembrane transporter activity / thyroid hormone transmembrane transporter activity / thyroid hormone transport / organic anion transmembrane transporter activity / bile acid transmembrane transporter activity / bile acid and bile salt transport / transport across blood-brain barrier / monoatomic ion transport / transmembrane transport / basolateral plasma membrane / plasma membrane
Similarity search - Function
Organic anion transporter polypeptide / Organic Anion Transporter Polypeptide (OATP) family / Kazal-type serine protease inhibitor domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
estrone 3-sulfate / Solute carrier organic anion transporter family member 1C1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGe, Y. / Yadav, G.P. / Jiang, J. / Huang, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM150878 United States
CitationJournal: To Be Published
Title: Structural insights into brain thyroid hormone transport via MCT8 and OATP1C1
Authors: Ge, Y. / Dou, T. / Nguyen, T.U. / Yadav, G.P. / Wensel, T.G. / Jiang, J. / Huang, P.
History
DepositionOct 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jul 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 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 organic anion transporter family member 1C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5154
Polymers82,4631
Non-polymers1,0513
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier organic anion transporter family member 1C1 / Organic anion transporter 1C1 / OATP1C1 / Organic anion transporter F / OATP-F / Organic anion ...Organic anion transporter 1C1 / OATP1C1 / Organic anion transporter F / OATP-F / Organic anion transporter polypeptide-related protein 5 / OAT-RP-5 / OATP-RP5 / Organic anion-transporting polypeptide 14 / OATP-14 / Solute carrier family 21 member 14 / Thyroxine transporter


Mass: 82463.227 Da / Num. of mol.: 1 / Mutation: F240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLCO1C1, OATP14, OATP1C1, OATPF, SLC21A14 / Production host: Homo sapiens (human) / References: UniProt: Q9NYB5
#2: Chemical ChemComp-FY5 / estrone 3-sulfate


Mass: 350.429 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H22O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, hormone*YM
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: human OATP1C1 F240A mutant in complex with estrone 3-sulfate
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.83 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249737 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 65.06 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00284385
ELECTRON MICROSCOPYf_angle_d0.83055962
ELECTRON MICROSCOPYf_chiral_restr0.0497685
ELECTRON MICROSCOPYf_plane_restr0.0054722
ELECTRON MICROSCOPYf_dihedral_angle_d7.5144635

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