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- EMDB-30870: Human bile salt exporter ABCB11 in complex with taurocholate -

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Basic information

Entry
Database: EMDB / ID: EMD-30870
TitleHuman bile salt exporter ABCB11 in complex with taurocholate
Map data
Sample
  • Complex: human ABCB11 in complex with taurocholate
    • Protein or peptide: Bile salt export pump
  • Ligand: TAUROCHOLIC ACID
KeywordsABC transporter / liver / MEMBRANE PROTEIN / TRANSLOCASE
Function / homology
Function and homology information


canalicular bile acid transmembrane transporter activity / positive regulation of bile acid secretion / Defective ABCB11 causes PFIC2 and BRIC2 / canalicular bile acid transport / intracellular canaliculus / regulation of fatty acid beta-oxidation / xenobiotic export from cell / regulation of bile acid metabolic process / ABC-type bile acid transporter activity / bile acid biosynthetic process ...canalicular bile acid transmembrane transporter activity / positive regulation of bile acid secretion / Defective ABCB11 causes PFIC2 and BRIC2 / canalicular bile acid transport / intracellular canaliculus / regulation of fatty acid beta-oxidation / xenobiotic export from cell / regulation of bile acid metabolic process / ABC-type bile acid transporter activity / bile acid biosynthetic process / xenobiotic transmembrane transport / phospholipid homeostasis / bile acid metabolic process / intercellular canaliculus / bile acid transmembrane transporter activity / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / bile acid and bile salt transport / lipid homeostasis / carbohydrate transmembrane transporter activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / xenobiotic metabolic process / cholesterol homeostasis / fatty acid metabolic process / : / recycling endosome / transmembrane transport / response to estrogen / recycling endosome membrane / response to oxidative stress / response to ethanol / endosome / protein ubiquitination / apical plasma membrane / Golgi membrane / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Bile salt export pump
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang L / How WT
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508500 China
CitationJournal: Cell Res / Year: 2022
Title: Structures of human bile acid exporter ABCB11 reveal a transport mechanism facilitated by two tandem substrate-binding pockets.
Authors: Liang Wang / Wen-Tao Hou / Jie Wang / Da Xu / Cong Guo / Linfeng Sun / Ke Ruan / Cong-Zhao Zhou / Yuxing Chen /
History
DepositionJan 12, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dv5
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30870.png

Downloads & links

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Map

FileDownload / File: emd_30870.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.)
1.01 Å/pix.
x 200 pix.
= 202. Å		1.01 Å/pix.
x 200 pix.
= 202. Å		1.01 Å/pix.
x 200 pix.
= 202. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.025
Minimum - Maximum-0.1034401 - 0.17340177
Average (Standard dev.)-0.00007038292 (±0.0066054906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 202.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.011.011.01
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z202.000202.000202.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1030.173-0.000

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Supplemental data

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Sample components

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Entire : human ABCB11 in complex with taurocholate

EntireName: human ABCB11 in complex with taurocholate
Components
  • Complex: human ABCB11 in complex with taurocholate
    • Protein or peptide: Bile salt export pump
  • Ligand: TAUROCHOLIC ACID

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Supramolecule #1: human ABCB11 in complex with taurocholate

SupramoleculeName: human ABCB11 in complex with taurocholate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 146 kDa/nm

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Macromolecule #1: Bile salt export pump

MacromoleculeName: Bile salt export pump / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140.872219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GFFQLFRFSS STDIWLMFVG SLCAFLHGIA QPGVLLIFGT MTDVFIDYDV ELQELQIPGK ACVNNTIVWT NSSLNQNMTN GTRCGLLNI ESEMIKFASY YAGIAVAVLI TGYIQICFWV IAAARQIQKM RKFYFRRIMR MEIGWFDCNS VGELNTRFSD D INKINDAI ...String:
GFFQLFRFSS STDIWLMFVG SLCAFLHGIA QPGVLLIFGT MTDVFIDYDV ELQELQIPGK ACVNNTIVWT NSSLNQNMTN GTRCGLLNI ESEMIKFASY YAGIAVAVLI TGYIQICFWV IAAARQIQKM RKFYFRRIMR MEIGWFDCNS VGELNTRFSD D INKINDAI ADQMALFIQR MTSTICGFLL GFFRGWKLTL VIISVSPLIG IGAATIGLSV SKFTDYELKA YAKAGVVADE VI SSMRTVA AFGGEKREVE RYEKNLVFAQ RWGIRKGIVM GFFTGFVWCL IFLCYALAFW YGSTLVLDEG EYTPGTLVQI FLS VIVGAL NLGNASPCLE AFATGRAAAT SIFETIDRKP IIDCMSEDGY KLDRIKGEIE FHNVTFHYPS RPEVKILNDL NMVI KPGEM TALVGPSGAG KSTALQLIQR FYDPCEGMVT VDGHDIRSLN IQWLRDQIGI VEQEPVLFST TIAENIRYGR EDATM EDIV QAAKEANAYN FIMDLPQQFD TLVGEGGGQM SGGQKQRVAI ARALIRNPKI LLLDMATSAL DNESEAMVQE VLSKIQ HGH TIISVAHRLS TVRAADTIIG FEHGTAVERG THEELLERKG VYFTLVTLQS QGNQALNEED IKDATEDDML ARTFSRG SY QDSLRASIRQ RSKSQLSYLV HEPPLAVVDH KSTYEEDRKD KDIPVQEEVE PAPVRRILKF SAPEWPYMLV GSVGAAVN G TVTPLYAFLF SQILGTFSIP DKEEQRSQIN GVCLLFVAMG CVSLFTQFLQ GYAFAKSGEL LTKRLRKFGF RAMLGQDIA WFDDLRNSPG ALTTRLATDA SQVQGAAGSQ IGMIVNSFTN VTVAMIIAFS FSWKLSLVIL CFFPFLALSG ATQTRMLTGF ASRDKQALE MVGQITNEAL SNIRTVAGIG KERRFIEALE TELEKPFKTA IQKANIYGFC FAFAQCIMFI ANSASYRYGG Y LISNEGLH FSYVFRVISA VVLSATALGR AFSYTPSYAK AKISAARFFQ LLDRQPPISV YNTAGEKWDN FQGKIDFVDC KF TYPSRPD SQVLNGLSVS ISPGQTLAFV GSSGCGKSTS IQLLERFYDP DQGKVMIDGH DSKKVNVQFL RSNIGIVSQE PVL FACSIM DNIKYGDNTK EIPMERVIAA AKQAQLHDFV MSLPEKYETN VGSQGSQLSR GEKQRIAIAR AIVRDPKILL LDEA TSALD TESEKTVQVA LDKAREGRTC IVIAHRLSTI QNADIIAVMA QGVVIEKGTH EELMAQKGAY YKLVT

UniProtKB: Bile salt export pump

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Macromolecule #2: TAUROCHOLIC ACID

MacromoleculeName: TAUROCHOLIC ACID / type: ligand / ID: 2 / Number of copies: 2 / Formula: TCH
Molecular weightTheoretical: 515.703 Da
Chemical component information

ChemComp-TCH:
TAUROCHOLIC ACID

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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

Concentration5.8 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 8 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2147192
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 100 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.10) / Number images used: 251574
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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