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- PDB-9unv: Cryo-EM structure of human organic solute transporter Ost-alpha/b... -

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Basic information

Entry
Database: PDB / ID: 9unv
TitleCryo-EM structure of human organic solute transporter Ost-alpha/beta bound with TLCA
Components(Organic solute transporter subunit ...) x 2
KeywordsTRANSPORT PROTEIN / Complex / bile acids
Function / homology
Function and homology information


: / bile acid secretion / positive regulation of protein exit from endoplasmic reticulum / bile acid transmembrane transporter activity / bile acid and bile salt transport / transmembrane transporter activity / positive regulation of protein targeting to membrane / Recycling of bile acids and salts / regulation of protein stability / basolateral plasma membrane ...: / bile acid secretion / positive regulation of protein exit from endoplasmic reticulum / bile acid transmembrane transporter activity / bile acid and bile salt transport / transmembrane transporter activity / positive regulation of protein targeting to membrane / Recycling of bile acids and salts / regulation of protein stability / basolateral plasma membrane / protein heterodimerization activity / endoplasmic reticulum membrane / protein homodimerization activity / protein-containing complex / membrane / plasma membrane
Similarity search - Function
Organic solute transporter subunit beta / : / Organic solute transporter subunit beta protein / Organic solute transporter subunit alpha/Transmembrane protein 184 / Organic solute transporter Ostalpha / Organic solute transporter Ostalpha
Similarity search - Domain/homology
Chem-76F / : / CHOLESTEROL / 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PHOSPHATIDYL ETHANOL / PALMITIC ACID / Organic solute transporter subunit alpha / Organic solute transporter subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsYang, X. / Xu, E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human organic solute transporter Ost-alpha/beta bound with TLCA
Authors: Yang, X. / Xu, E.
History
DepositionApr 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 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: Organic solute transporter subunit alpha
B: Organic solute transporter subunit beta
C: Organic solute transporter subunit alpha
D: Organic solute transporter subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,29856
Polymers109,8224
Non-polymers20,47652
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

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Organic solute transporter subunit ... , 2 types, 4 molecules ACBD

#1: Protein Organic solute transporter subunit alpha / OST-alpha / Solute carrier family 51 subunit alpha


Mass: 38967.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NAG and PLM is the modification on the residues of the chain
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC51A, OSTA / Production host: Homo sapiens (human) / References: UniProt: Q86UW1
#2: Protein Organic solute transporter subunit beta / OST-beta / Solute carrier family 51 subunit beta


Mass: 15943.913 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC51B, OSTB / Production host: Homo sapiens (human) / References: UniProt: Q86UW2

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Sugars , 1 types, 2 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 50 molecules

#3: Chemical...
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-P0E / PHOSPHATIDYL ETHANOL / (2S)-2-[(9E)-HEXADEC-9-ENOYLOXY]-3-{[HYDROXY(2-HYDROXYETHOXY)PHOSPHORYL]OXY}PROPYL (9E)-OCTADEC-9-ENOATE


Mass: 716.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H73O9P
#5: Chemical ChemComp-LPE / 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / LPC-ETHER


Mass: 510.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H57NO6P
#7: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C16H32O2
#8: Chemical ChemComp-A1EPX / Taurolithocholic Acid


Mass: 483.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H45NO5S
#9: Chemical
ChemComp-76F / (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate / DOPE


Mass: 742.018 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H76NO8P / Feature type: SUBJECT OF INVESTIGATION

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Details

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: Homo dimer of dimerized Ost-alpha and Ost-beta / Type: COMPLEX / Entity ID: #1-#2 / 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: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.6.2particle selectionBlob pick and template pick
13cryoSPARC4.6.23D reconstructionLocal refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76705 / Symmetry type: POINT

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