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Yorodumi- PDB-8rq3: Cryo-em structure of the rat Multidrug resistance-associated prot... -
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-Basic information
Entry | Database: PDB / ID: 8rq3 | ||||||
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Title | Cryo-em structure of the rat Multidrug resistance-associated protein 2 (rMrp2) in an autoinhibited state (nucleotide-free) | ||||||
Components | ATP-binding cassette sub-family C member 2 | ||||||
Keywords | TRANSPORT PROTEIN / Multidrug resistance-associated protein 2 (rMrp2) in an autoinhibited state (nucleotide-free) | ||||||
Function / homology | Function and homology information mercury ion transport / benzylpenicillin metabolic process / Aspirin ADME / Paracetamol ADME / Atorvastatin ADME / canalicular bile acid transport / intracellular canaliculus / antibiotic metabolic process / bilirubin transmembrane transporter activity / bilirubin transport ...mercury ion transport / benzylpenicillin metabolic process / Aspirin ADME / Paracetamol ADME / Atorvastatin ADME / canalicular bile acid transport / intracellular canaliculus / antibiotic metabolic process / bilirubin transmembrane transporter activity / bilirubin transport / xenobiotic export from cell / Heme degradation / response to antineoplastic agent / leukotriene transport / thyroid hormone transport / prostaglandin transport / detoxification of mercury ion / ABC-family proteins mediated transport / regulation of bile acid secretion / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / intracellular chloride ion homeostasis / organic anion transport / xenobiotic transmembrane transport / organic anion transmembrane transporter activity / xenobiotic transport across blood-brain barrier / transepithelial transport / xenobiotic detoxification by transmembrane export across the plasma membrane / intercellular canaliculus / ABC-type xenobiotic transporter / response to arsenic-containing substance / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / bile acid and bile salt transport / cellular response to interleukin-6 / ABC-type xenobiotic transporter activity / response to glucagon / bile acid signaling pathway / response to steroid hormone / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / cellular response to interleukin-1 / xenobiotic catabolic process / cellular response to dexamethasone stimulus / female pregnancy / brush border membrane / response to organic cyclic compound / transmembrane transport / response to estrogen / cellular response to xenobiotic stimulus / response to estradiol / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to oxidative stress / response to lipopolysaccharide / response to xenobiotic stimulus / apical plasma membrane / protein domain specific binding / negative regulation of gene expression / cell surface / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å | ||||||
Authors | Mazza, T. / Beis, K. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for the modulation of MRP2 activity by phosphorylation and drugs. Authors: Tiziano Mazza / Theodoros I Roumeliotis / Elena Garitta / David Drew / S Tamir Rashid / Cesare Indiveri / Jyoti S Choudhary / Kenneth J Linton / Konstantinos Beis / Abstract: Multidrug resistance-associated protein 2 (MRP2/ABCC2) is a polyspecific efflux transporter of organic anions expressed in hepatocyte canalicular membranes. MRP2 dysfunction, in Dubin-Johnson ...Multidrug resistance-associated protein 2 (MRP2/ABCC2) is a polyspecific efflux transporter of organic anions expressed in hepatocyte canalicular membranes. MRP2 dysfunction, in Dubin-Johnson syndrome or by off-target inhibition, for example by the uricosuric drug probenecid, elevates circulating bilirubin glucuronide and is a cause of jaundice. Here, we determine the cryo-EM structure of rat Mrp2 (rMrp2) in an autoinhibited state and in complex with probenecid. The autoinhibited state exhibits an unusual conformation for this class of transporter in which the regulatory domain is folded within the transmembrane domain cavity. In vitro phosphorylation, mass spectrometry and transport assays show that phosphorylation of the regulatory domain relieves this autoinhibition and enhances rMrp2 transport activity. The in vitro data is confirmed in human hepatocyte-like cells, in which inhibition of endogenous kinases also reduces human MRP2 transport activity. The drug-bound state reveals two probenecid binding sites that suggest a dynamic interplay with autoinhibition. Mapping of the Dubin-Johnson mutations onto the rodent structure indicates that many may interfere with the transition between conformational states. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rq3.cif.gz | 261.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rq3.ent.gz | 207.4 KB | Display | PDB format |
PDBx/mmJSON format | 8rq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rq3_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8rq3_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8rq3_validation.xml.gz | 52.1 KB | Display | |
Data in CIF | 8rq3_validation.cif.gz | 75.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/8rq3 ftp://data.pdbj.org/pub/pdb/validation_reports/rq/8rq3 | HTTPS FTP |
-Related structure data
Related structure data | 19431MC 8rq4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 173571.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Abcc2, Cmoat, Cmrp, Mrp2 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: Q63120, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate, ABC-type xenobiotic transporter, ABC-type ...References: UniProt: Q63120, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate, ABC-type xenobiotic transporter, ABC-type glutathione-S-conjugate transporter |
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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: rat Multidrug resistance-associated protein 2 (rMrp2) in an autoinhibited state (nucleotide-free) Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
Specimen | 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 / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 49.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282209 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Atomic model building | Accession code: AF-Q63120-F1 / Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
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