+Open data
-Basic information
Entry | Database: PDB / ID: 7oti | ||||||
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Title | Structure of ABCB1/P-glycoprotein in apo state | ||||||
Components | Multidrug resistance protein 1A | ||||||
Keywords | MEMBRANE PROTEIN / ABCB1 / ABC Transporters / Membrane Proteins / Ivacaftor / MDR1 / Multidrug resistance / cryo-em | ||||||
Function / homology | Function and homology information hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / response to quercetin / negative regulation of sensory perception of pain ...hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / response to quercetin / negative regulation of sensory perception of pain / regulation of intestinal absorption / cellular response to external biotic stimulus / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / Prednisone ADME / terpenoid transport / ceramide floppase activity / response to glycoside / ceramide translocation / floppase activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / response to alcohol / ABC-family proteins mediated transport / phosphatidylethanolamine flippase activity / response to thyroxine / establishment of blood-brain barrier / phosphatidylcholine floppase activity / xenobiotic transport across blood-brain barrier / export across plasma membrane / ABC-type xenobiotic transporter / xenobiotic detoxification by transmembrane export across the plasma membrane / cellular response to L-glutamate / intercellular canaliculus / P-type phospholipid transporter / response to vitamin D / ABC-type xenobiotic transporter activity / response to vitamin A / intestinal absorption / response to glucagon / phospholipid translocation / cellular response to antibiotic / cellular hyperosmotic salinity response / maintenance of blood-brain barrier / cellular response to alkaloid / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / cellular response to estradiol stimulus / response to progesterone / female pregnancy / brush border membrane / placenta development / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Ford, R.C. / Barbieri, A. / Thonghin, N. / Shafi, T. / Prince, S.M. / Collins, R.F. | ||||||
Funding support | 1items
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Citation | Journal: Membranes (Basel) / Year: 2021 Title: Structure of ABCB1/P-Glycoprotein in the Presence of the CFTR Potentiator Ivacaftor. Authors: Alessandro Barbieri / Nopnithi Thonghin / Talha Shafi / Stephen M Prince / Richard F Collins / Robert C Ford / Abstract: ABCB1/P-glycoprotein is an ATP binding cassette transporter that is involved in the clearance of xenobiotics, and it affects the disposition of many drugs in the body. Conformational flexibility of ...ABCB1/P-glycoprotein is an ATP binding cassette transporter that is involved in the clearance of xenobiotics, and it affects the disposition of many drugs in the body. Conformational flexibility of the protein within the membrane is an intrinsic part of its mechanism of action, but this has made structural studies challenging. Here, we have studied different conformations of P-glycoprotein simultaneously in the presence of ivacaftor, a known competitive inhibitor. In order to conduct this, we used high contrast cryo-electron microscopy imaging with a Volta phase plate. We associate the presence of ivacaftor with the appearance of an additional density in one of the conformational states detected. The additional density is in the central aqueous cavity and is associated with a wider separation of the two halves of the transporter in the inward-facing state. Conformational changes to the nucleotide-binding domains are also observed and may help to explain the stimulation of ATPase activity that occurs when transported substrate is bound in many ATP binding cassette transporters. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7oti.cif.gz | 210.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oti.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 7oti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oti_validation.pdf.gz | 902.4 KB | Display | wwPDB validaton report |
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Full document | 7oti_full_validation.pdf.gz | 912.8 KB | Display | |
Data in XML | 7oti_validation.xml.gz | 35 KB | Display | |
Data in CIF | 7oti_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/7oti ftp://data.pdbj.org/pub/pdb/validation_reports/ot/7oti | HTTPS FTP |
-Related structure data
Related structure data | 13060MC 7otgC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 141877.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 / Production host: Komagataella pastoris (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Structure of ABCB1/P-glycoprotein in apo state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Komagataella pastoris (fungus) |
Buffer solution | pH: 8 |
Specimen | Conc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Phase plate: VOLTA PHASE PLATE / Spherical aberration corrector: 2.7 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Particle selection | Num. of particles selected: 317000 | ||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104000 / Symmetry type: POINT |