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- PDB-9dxp: Cryo-EM structure of human OATP1C1 in complex with thyroid hormone T4 -

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Basic information

Entry
Database: PDB / ID: 9dxp
TitleCryo-EM structure of human OATP1C1 in complex with thyroid hormone T4
ComponentsSolute carrier organic anion transporter family member 1C1
KeywordsTRANSPORT PROTEIN / SLC transporter / thyroid hormone
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
3,5,3',5'-TETRAIODO-L-THYRONINE / CHOLESTEROL HEMISUCCINATE / Solute carrier organic anion transporter family member 1C1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsGe, Y. / Dou, T. / 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

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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)83,8033
Polymers82,5391
Non-polymers1,2642
Water362
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: 82539.328 Da / Num. of mol.: 1
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-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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 in complex with thyroid hormone T4 / 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: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 454807 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 31.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00364386
ELECTRON MICROSCOPYf_angle_d0.65225950
ELECTRON MICROSCOPYf_chiral_restr0.0445680
ELECTRON MICROSCOPYf_plane_restr0.0061726
ELECTRON MICROSCOPYf_dihedral_angle_d8.2263624

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