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- EMDB-12367: Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posac... -

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Basic information

Entry
Database: EMDB / ID: EMD-12367
TitleNanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound, inward-open conformation)
Map dataNanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound, inward-open conformation)
Sample
  • Complex: Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound, inward-open conformation)
    • Complex: phosphatidylcholine translocator ABCB4
      • Protein or peptide: Phosphatidylcholine translocator ABCB4
    • Complex: 4B1 Fab-fragment: light chain
      • Protein or peptide: 4B1 Fab-fragment light chain
    • Complex: 4B1 Fab-fragment: heavy chain
      • Protein or peptide: 4B1 Fab-fragment heavy chain
  • Ligand: CHOLESTEROL
  • Ligand: POSACONAZOLE
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
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 / phospholipid transporter activity / bile acid secretion / cellular response to bile acid / phosphatidylcholine floppase activity / intercellular canaliculus ...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 / phospholipid transporter activity / bile acid secretion / cellular response to bile acid / phosphatidylcholine floppase activity / intercellular canaliculus / P-type phospholipid transporter / phospholipid translocation / clathrin-coated vesicle / lipid homeostasis / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / ABC-family proteins mediated transport / lipid metabolic process / transmembrane transport / PPARA activates gene expression / membrane raft / apical plasma membrane / focal adhesion / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
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: 3.8 Å
AuthorsNosol K / Locher KP
Funding support Switzerland, United States, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_189111 Switzerland
Swiss National Science Foundation310030_155563 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117372 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structures of ABCB4 provide insight into phosphatidylcholine translocation.
Authors: Kamil Nosol / Rose Bang-Sørensen / Rossitza N Irobalieva / Satchal K Erramilli / Bruno Stieger / Anthony A Kossiakoff / Kaspar P Locher /
Abstract: ABCB4 is expressed in hepatocytes and translocates phosphatidylcholine into bile canaliculi. The mechanism of specific lipid recruitment from the canalicular membrane, which is essential to mitigate ...ABCB4 is expressed in hepatocytes and translocates phosphatidylcholine into bile canaliculi. The mechanism of specific lipid recruitment from the canalicular membrane, which is essential to mitigate the cytotoxicity of bile salts, is poorly understood. We present cryogenic electron microscopy structures of human ABCB4 in three distinct functional conformations. An apo-inward structure reveals how phospholipid can be recruited from the inner leaflet of the membrane without flipping its orientation. An occluded structure reveals a single phospholipid molecule in a central cavity. Its choline moiety is stabilized by cation-π interactions with an essential tryptophan residue, rationalizing the specificity of ABCB4 for phosphatidylcholine. In an inhibitor-bound structure, a posaconazole molecule blocks phospholipids from reaching the central cavity. Using a proteoliposome-based translocation assay with fluorescently labeled phosphatidylcholine analogs, we recapitulated the substrate specificity of ABCB4 in vitro and confirmed the role of the key tryptophan residue. Our results provide a structural basis for understanding an essential translocation step in the generation of bile and its sensitivity to azole drugs.
History
DepositionFeb 14, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7niw
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12367.png

Downloads & links

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Map

FileDownload / File: emd_12367.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound, inward-open conformation)
Voxel sizeX=Y=Z: 0.66 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.03721011 - 0.05489589
Average (Standard dev.)-1.3030514e-06 (±0.001316088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 295.68002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.660.660.66
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z295.680295.680295.680
α/β/γ90.00090.00090.000
start NX/NY/NZ383838
NX/NY/NZ225225225
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0370.055-0.000

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Supplemental data

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Sample components

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Entire : Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posac...

EntireName: Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound, inward-open conformation)
Components
  • Complex: Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound, inward-open conformation)
    • Complex: phosphatidylcholine translocator ABCB4
      • Protein or peptide: Phosphatidylcholine translocator ABCB4
    • Complex: 4B1 Fab-fragment: light chain
      • Protein or peptide: 4B1 Fab-fragment light chain
    • Complex: 4B1 Fab-fragment: heavy chain
      • Protein or peptide: 4B1 Fab-fragment heavy chain
  • Ligand: CHOLESTEROL
  • Ligand: POSACONAZOLE
  • Ligand: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posac...

SupramoleculeName: Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound, inward-open conformation)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 140 KDa

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Supramolecule #2: phosphatidylcholine translocator ABCB4

SupramoleculeName: phosphatidylcholine translocator ABCB4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: 4B1 Fab-fragment: light chain

SupramoleculeName: 4B1 Fab-fragment: light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: 4B1 Fab-fragment: heavy chain

SupramoleculeName: 4B1 Fab-fragment: heavy chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

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Macromolecule #2: 4B1 Fab-fragment light chain

MacromoleculeName: 4B1 Fab-fragment light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.346957 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQGYSKLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQGYSKLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: 4B1 Fab-fragment heavy chain

MacromoleculeName: 4B1 Fab-fragment heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.754572 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NLYSSYIHWV RQAPGKGLEW VAYISSYYGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSFSINGSY SWWWDQAAYG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NLYSSYIHWV RQAPGKGLEW VAYISSYYGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSFSINGSY SWWWDQAAYG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK TH T

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #5: POSACONAZOLE

MacromoleculeName: POSACONAZOLE / type: ligand / ID: 5 / Number of copies: 1 / Formula: X2N
Molecular weightTheoretical: 700.777 Da
Chemical component information

ChemComp-X2N:
POSACONAZOLE / medication, antifungal*YM / Posaconazole

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Macromolecule #6: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DLP
Molecular weightTheoretical: 782.082 Da
Chemical component information

ChemComp-DLP:
1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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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

Concentration0.48 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90891
FSC plot (resolution estimation)

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