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- EMDB-66180: cryo-EM structure of human organic solute transporter in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66180
Titlecryo-EM structure of human organic solute transporter in complex with fidaxomicin
Map data
Sample
  • Complex: cryo-EM structure of organic solute transporter in complex with fidaxomicin
    • Protein or peptide: Organic solute transporter subunit beta
    • Protein or peptide: Organic solute transporter subunit alpha
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: Fidaxomicin
Keywordsfidaxomicin / TRANSPORTER / TRANSPORT PROTEIN
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
Organic solute transporter subunit alpha / Organic solute transporter subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsSun X / Yao D / Xue J
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66180.png

Downloads & links

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Map

FileDownload / File: emd_66180.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.9187862 - 3.1350236
Average (Standard dev.)0.002826469 (±0.07940547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66180_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66180_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cryo-EM structure of organic solute transporter in complex with f...

EntireName: cryo-EM structure of organic solute transporter in complex with fidaxomicin
Components
  • Complex: cryo-EM structure of organic solute transporter in complex with fidaxomicin
    • Protein or peptide: Organic solute transporter subunit beta
    • Protein or peptide: Organic solute transporter subunit alpha
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: Fidaxomicin

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Supramolecule #1: cryo-EM structure of organic solute transporter in complex with f...

SupramoleculeName: cryo-EM structure of organic solute transporter in complex with fidaxomicin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Organic solute transporter subunit beta

MacromoleculeName: Organic solute transporter subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.361263 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEHSEGAPGD PAGTVVPQEL LEEMLWFFRV EDASPWNHSI LALAAVVVII SMVLLGRSIQ ASRKEKMQPP EKETPEVLHL DEAKDHNSL NNLRETLLSE KPNLAQVELE LKERDVLSVF LPDVPETES

UniProtKB: Organic solute transporter subunit beta

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Macromolecule #2: Organic solute transporter subunit alpha

MacromoleculeName: Organic solute transporter subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.768938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPGRTQIKL DPRYTADLLE VLKTNYGIPS ACFSQPPTAA QLLRALGPVE LALTSILTLL ALGSIAIFLE DAVYLYKNTL CPIKRRTLL WKSSAPTVVS VLCCFGLWIP RSLVLVEMTI TSFYAVCFYL LMLVMVEGFG GKEAVLRTLR DTPMMVHTGP C CCCCPCCP ...String:
MEPGRTQIKL DPRYTADLLE VLKTNYGIPS ACFSQPPTAA QLLRALGPVE LALTSILTLL ALGSIAIFLE DAVYLYKNTL CPIKRRTLL WKSSAPTVVS VLCCFGLWIP RSLVLVEMTI TSFYAVCFYL LMLVMVEGFG GKEAVLRTLR DTPMMVHTGP C CCCCPCCP RLLLTRKKLQ LLMLGPFQYA FLKITLTLVG LFLVPDGIYD PADISEGSTA LWINTFLGVS TLLALWTLGI IS RQARLHL GEQNMGAKFA LFQVLLILTA LQPSIFSVLA NGGQIACSPP YSSKTRSQVM NCHLLILETF LMTVLTRMYY RRK DHKVGY ETFSSPDLDL NLKA

UniProtKB: Organic solute transporter subunit alpha

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 12 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 14 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 5 / Number of copies: 6 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #6: Fidaxomicin

MacromoleculeName: Fidaxomicin / type: ligand / ID: 6 / Number of copies: 2 / Formula: FI8
Molecular weightTheoretical: 1.058039 KDa
Chemical component information

ChemComp-FI8:
Fidaxomicin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.9 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 689213
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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