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- EMDB-63149: transport AD -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63149
Titletransport AD
Map data
Sample
  • Complex: Transport AD
    • Protein or peptide: Organic solute transporter subunit beta
    • Protein or peptide: Organic solute transporter subunit alpha
  • Ligand: PALMITIC ACID
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 17-oxoandrost-5-en-3beta-yl hydrogen sulfate
Keywordstransport AD / TRANSPORT PROTEIN
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
Organic solute transporter subunit alpha / Organic solute transporter subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsWang K / Jiang DH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: To Be Published
Title: transport AD
Authors: Wang K / Jiang DH
History
DepositionJan 15, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63149.png

Downloads & links

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Map

FileDownload / File: emd_63149.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.451
Minimum - Maximum-1.7719816 - 2.775341
Average (Standard dev.)-0.00021014956 (±0.052760232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63149_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_63149_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 : Transport AD

EntireName: Transport AD
Components
  • Complex: Transport AD
    • Protein or peptide: Organic solute transporter subunit beta
    • Protein or peptide: Organic solute transporter subunit alpha
  • Ligand: PALMITIC ACID
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 17-oxoandrost-5-en-3beta-yl hydrogen sulfate

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Supramolecule #1: Transport AD

SupramoleculeName: Transport AD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Organic solute transporter subunit alpha

MacromoleculeName: Organic solute transporter subunit alpha / type: protein_or_peptide / ID: 1 / 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 #2: Organic solute transporter subunit beta

MacromoleculeName: Organic solute transporter subunit beta / type: protein_or_peptide / ID: 2 / 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 #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 14 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #4: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 4 / Number of copies: 4 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 8 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #6: 17-oxoandrost-5-en-3beta-yl hydrogen sulfate

MacromoleculeName: 17-oxoandrost-5-en-3beta-yl hydrogen sulfate / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZWY
Molecular weightTheoretical: 368.488 Da
Chemical component information

ChemComp-ZWY:
17-oxoandrost-5-en-3beta-yl hydrogen sulfate

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 189210
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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