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- PDB-9wqr: cryo-EM structure of human organic solute transporter in complex ... -

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Basic information

Entry
Database: PDB / ID: 9wqr
Titlecryo-EM structure of human organic solute transporter in complex with fidaxomicin
Components(Organic solute transporter subunit ...) x 2
KeywordsTRANSPORT PROTEIN / fidaxomicin / TRANSPORTER
Function / homology
Function and homology information


bile acid secretion / positive regulation of protein exit from endoplasmic reticulum / positive regulation of glycoprotein biosynthetic process / bile acid transmembrane transporter activity / bile acid and bile salt transport / positive regulation of protein targeting to membrane / transmembrane transporter activity / Recycling of bile acids and salts / regulation of protein stability / basolateral plasma membrane ...bile acid secretion / positive regulation of protein exit from endoplasmic reticulum / positive regulation of glycoprotein biosynthetic process / bile acid transmembrane transporter activity / bile acid and bile salt transport / positive regulation of protein targeting to membrane / transmembrane transporter activity / 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
CHOLESTEROL / Fidaxomicin / PALMITIC ACID / Chem-POV / 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: 2.79 Å
AuthorsSun, X. / Yao, D. / Xue, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NCTIB2022HS02004 China
CitationJournal: To Be Published
Title: cryo-EM structure of human organic solute transporter in complex with fidaxomicin
Authors: Sun, X. / Yao, D. / Xue, J.
History
DepositionSep 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data 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
B: Organic solute transporter subunit beta
A: Organic solute transporter subunit alpha
C: Organic solute transporter subunit alpha
D: Organic solute transporter subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,16738
Polymers104,2604
Non-polymers14,90634
Water00
1


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

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Components

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

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


Mass: 14361.263 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
#2: Protein Organic solute transporter subunit alpha / OST-alpha / Solute carrier family 51 subunit alpha


Mass: 37768.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC51A, OSTA / Production host: Homo sapiens (human) / References: UniProt: Q86UW1

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Non-polymers , 4 types, 34 molecules

#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-FI8 / Fidaxomicin


Mass: 1058.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C52H74Cl2O18 / 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: cryo-EM structure of organic solute transporter in complex with fidaxomicin
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

MicroscopyModel: FEI/PHILIPS CM300FEG/T
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 689213 / Symmetry type: POINT
RefinementHighest resolution: 2.79 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037080
ELECTRON MICROSCOPYf_angle_d0.7089550
ELECTRON MICROSCOPYf_dihedral_angle_d15.6632200
ELECTRON MICROSCOPYf_chiral_restr0.0361130
ELECTRON MICROSCOPYf_plane_restr0.0061042

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