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Yorodumi- PDB-6bhu: Cryo-EM structure of ATP-bound, outward-facing bovine multidrug r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bhu | ||||||||||||
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Title | Cryo-EM structure of ATP-bound, outward-facing bovine multidrug resistance protein 1 (MRP1) | ||||||||||||
Components | Multidrug resistance-associated protein 1 | ||||||||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / multidrug resistance / outward facing | ||||||||||||
Function / homology | Function and homology information Sphingolipid de novo biosynthesis / Heme degradation / Synthesis of Leukotrienes (LT) and Eoxins (EX) / cyclic nucleotide transport / Transport of RCbl within the body / Paracetamol ADME / leukotriene transport / glutathione transmembrane transport / glutathione transmembrane transporter activity / ABC-type glutathione-S-conjugate transporter ...Sphingolipid de novo biosynthesis / Heme degradation / Synthesis of Leukotrienes (LT) and Eoxins (EX) / cyclic nucleotide transport / Transport of RCbl within the body / Paracetamol ADME / leukotriene transport / glutathione transmembrane transport / glutathione transmembrane transporter activity / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / ABC-family proteins mediated transport / Cytoprotection by HMOX1 / ABC-type xenobiotic transporter / xenobiotic transport / ABC-type xenobiotic transporter activity / lipid transport / xenobiotic transmembrane transporter activity / ABC-type transporter activity / positive regulation of inflammatory response / basolateral plasma membrane / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å | ||||||||||||
Authors | Johnson, Z.L. / Chen, J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Cell / Year: 2018 Title: ATP Binding Enables Substrate Release from Multidrug Resistance Protein 1. Authors: Zachary Lee Johnson / Jue Chen / Abstract: The multidrug resistance protein MRP1 is an ATP-driven pump that confers resistance to chemotherapy. Previously, we have shown that intracellular substrates are recruited to a bipartite binding site ...The multidrug resistance protein MRP1 is an ATP-driven pump that confers resistance to chemotherapy. Previously, we have shown that intracellular substrates are recruited to a bipartite binding site when the transporter rests in an inward-facing conformation. A key question remains: how are high-affinity substrates transferred across the membrane and released outside the cell? Using electron cryomicroscopy, we show here that ATP binding opens the transport pathway to the extracellular space and reconfigures the substrate-binding site such that it relinquishes its affinity for substrate. Thus, substrate is released prior to ATP hydrolysis. With this result, we now have a complete description of the conformational cycle that enables substrate transfer in a eukaryotic ABC exporter. | ||||||||||||
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 | 6bhu.cif.gz | 280.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bhu.ent.gz | 212.4 KB | Display | PDB format |
PDBx/mmJSON format | 6bhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bhu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6bhu_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6bhu_validation.xml.gz | 46 KB | Display | |
Data in CIF | 6bhu_validation.cif.gz | 68.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/6bhu ftp://data.pdbj.org/pub/pdb/validation_reports/bh/6bhu | HTTPS FTP |
-Related structure data
Related structure data | 7099MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 183074.062 Da / Num. of mol.: 1 / Mutation: E1454Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ABCC1, MRP1 / Cell line (production host): HEK293S GntI- / Production host: Homo sapiens (human) / References: UniProt: Q8HXQ5 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | Sequence details | RESIDUES 30-194, CORRESPONDING TO TMD0, ARE MODELED AS POLY- ALANINE (POLY UNK). THE REGISTER IN ...RESIDUES 30-194, CORRESPOND | |
-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: bovine multidrug resistance protein 1 (MRP1) E1454Q / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.17 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Bos taurus (cattle) | ||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293S GntI- / Plasmid: Baculovirus | ||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD Grid type: Quantifoil R1.2/1.3 400-mesh Au Holey Carbon Grids | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-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 magnification: 37000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K |
Image recording | Average exposure time: 7 sec. / Electron dose: 84 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4210 |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
Software | Name: REFMAC / Version: 5.8.0158 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 354752 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354752 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.14→142 Å / Cor.coef. Fo:Fc: 0.969 / ESU R: 0.43 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 204.276 Å2
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Refinement step | Cycle: 1 / Total: 10273 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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