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- EMDB-10111: Nucleotide bound ABCB4 -

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Basic information

Entry
Database: EMDB / ID: EMD-10111
TitleNucleotide bound ABCB4
Map dataSingle-particle cryo-em map of nucleotide-bound ABCB4
Sample
  • Complex: Nucleotide Bound ABCB4
    • Protein or peptide: Phosphatidylcholine translocator ABCB4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL
KeywordsABC Transporter / Lipid extruder / TRANSPORT PROTEIN
Function / homology
Function and homology information


response to fenofibrate / Defective ABCB4 causes PFIC3, ICP3 and GBD1 / positive regulation of phospholipid transport / positive regulation of cholesterol transport / positive regulation of phospholipid translocation / bile acid secretion / phospholipid transporter activity / cellular response to bile acid / ABC-type oligopeptide transporter activity / phosphatidylcholine floppase activity ...response to fenofibrate / Defective ABCB4 causes PFIC3, ICP3 and GBD1 / positive regulation of phospholipid transport / positive regulation of cholesterol transport / positive regulation of phospholipid translocation / bile acid secretion / phospholipid transporter activity / cellular response to bile acid / ABC-type oligopeptide transporter activity / phosphatidylcholine floppase activity / intercellular canaliculus / P-type phospholipid transporter / phospholipid translocation / clathrin-coated vesicle / lipid homeostasis / ATPase-coupled transmembrane transporter activity / ABC-family proteins mediated transport / lipid metabolic process / PPARA activates gene expression / transmembrane transport / membrane raft / apical plasma membrane / focal adhesion / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
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
Phosphatidylcholine translocator ABCB4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsOlsen JA / Alam A
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4181-00021 Denmark
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structure of the human lipid exporter ABCB4 in a lipid environment.
Authors: Jeppe A Olsen / Amer Alam / Julia Kowal / Bruno Stieger / Kaspar P Locher /
Abstract: ABCB4 is an ATP-binding cassette transporter that extrudes phosphatidylcholine into the bile canaliculi of the liver. Its dysfunction or inhibition by drugs can cause severe, chronic liver disease or ...ABCB4 is an ATP-binding cassette transporter that extrudes phosphatidylcholine into the bile canaliculi of the liver. Its dysfunction or inhibition by drugs can cause severe, chronic liver disease or drug-induced liver injury. We determined the cryo-EM structure of nanodisc-reconstituted human ABCB4 trapped in an ATP-bound state at a resolution of 3.2 Å. The nucleotide binding domains form a closed conformation containing two bound ATP molecules, but only one of the ATPase sites contains bound Mg. The transmembrane domains adopt a collapsed conformation at the level of the lipid bilayer, but we observed a large, hydrophilic and fully occluded cavity at the level of the cytoplasmic membrane boundary, with no ligand bound. This indicates a state following substrate release but prior to ATP hydrolysis. Our results rationalize disease-causing mutations in human ABCB4 and suggest an 'alternating access' mechanism of lipid extrusion, distinct from the 'credit card swipe' model of other lipid transporters.
History
DepositionJul 5, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseDec 25, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / 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
  • Download
  • 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-6s7p
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10111.png

Downloads & links

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Map

FileDownload / File: emd_10111.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-particle cryo-em map of nucleotide-bound ABCB4
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.025
Minimum - Maximum-0.07880121 - 0.14066027
Average (Standard dev.)-0.00000033232962 (±0.0036481246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0790.141-0.000

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Supplemental data

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Sample components

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Entire : Nucleotide Bound ABCB4

EntireName: Nucleotide Bound ABCB4
Components
  • Complex: Nucleotide Bound ABCB4
    • Protein or peptide: Phosphatidylcholine translocator ABCB4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL

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Supramolecule #1: Nucleotide Bound ABCB4

SupramoleculeName: Nucleotide Bound ABCB4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 141 KDa

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Macromolecule #1: Phosphatidylcholine translocator ABCB4

MacromoleculeName: Phosphatidylcholine translocator ABCB4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140.833406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDLEAAKNGT AWRPTSAEGD FELGISSKQK RKKTKTVKMI GVLTLFRYSD WQDKLFMSLG TIMAIAHGSG LPLMMIVFGE MTDKFVDTA GNFSFPVNFS LSLLNPGKIL EEEMTRYAYY YSGLGAGVLV AAYIQVSFWT LAAGRQIRKI RQKFFHAILR Q EIGWFDIN ...String:
MDLEAAKNGT AWRPTSAEGD FELGISSKQK RKKTKTVKMI GVLTLFRYSD WQDKLFMSLG TIMAIAHGSG LPLMMIVFGE MTDKFVDTA GNFSFPVNFS LSLLNPGKIL EEEMTRYAYY YSGLGAGVLV AAYIQVSFWT LAAGRQIRKI RQKFFHAILR Q EIGWFDIN DTTELNTRLT DDISKISEGI GDKVGMFFQA VATFFAGFIV GFIRGWKLTL VIMAISPILG LSAAVWAKIL SA FSDKELA AYAKAGAVAE EALGAIRTVI AFGGQNKELE RYQKHLENAK EIGIKKAISA NISMGIAFLL IYASYALAFW YGS TLVISK EYTIGNAMTV FFSILIGAFS VGQAAPCIDA FANARGAAYV IFDIIDNNPK IDSFSERGHK PDSIKGNLEF NDVH FSYPS RANVKILKGL NLKVQSGQTV ALVGSSGCGK STTVQLIQRL YDPDEGTINI DGQDIRNFNV NYLREIIGVV SQEPV LFST TIAENICYGR GNVTMDEIKK AVKEANAYEF IMKLPQKFDT LVGERGAQLS GGQKQRIAIA RALVRNPKIL LLDQAT SAL DTESEAEVQA ALDKAREGRT TIVIAHRLST VRNADVIAGF EDGVIVEQGS HSELMKKEGV YFKLVNMQTS GSQIQSE EF ELNDEKAATR MAPNGWKSRL FRHSTQKNLK NSQMCQKSLD VETDGLEANV PPVSFLKVLK LNKTEWPYFV VGTVCAIA N GGLQPAFSVI FSEIIAIFGP GDDAVKQQKC NIFSLIFLFL GIISFFTFFL QGFTFGKAGE ILTRRLRSMA FKAMLRQDM SWFDDHKNST GALSTRLATD AAQVQGATGT RLALIAQNIA NLGTGIIISF IYGWQLTLLL LAVVPIIAVS GIVEMKLLAG NAKRDKKEL EAAGKIATEA IENIRTVVSL TQERKFESMY VEKLYGPYRN SVQKAHIYGI TFSISQAFMY FSYAGCFRFG A YLIVNGHM RFRDVILVFS AIVFGAVALG HASSFAPDYA KAKLSAAHLF MLFERQPLID SYSEEGLKPD KFEGNITFNE VV FNYPTRA NVPVLQGLSL EVKKGQTLAL VGSSGCGKST VVQLLERFYD PLAGTVLLDG QEAKKLNVQW LRAQLGIVSQ EPI LFDCSI AENIAYGDNS RVVSQDEIVS AAKAANIHPF IETLPHKYET RVGDKGTQLS GGQKQRIAIA RALIRQPQIL LLDQ ATSAL DTESEKVVQE ALDKAREGRT CIVIAHRLST IQNADLIVVF QNGRVKEHGT HQQLLAQKGI YFSMVSVQAG TQNL

UniProtKB: Phosphatidylcholine translocator ABCB4

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 8 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium Chloride
5.0 mMMgCl2+Magnesium Chloride
5.0 mMC10H16N5O13P3ATP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details5mM Magnesium Chloride 5mM ATP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 193929
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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