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Yorodumi- PDB-8b7v: Automated simulation-based refinement of maltoporin into a cryo-E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b7v | |||||||||
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Title | Automated simulation-based refinement of maltoporin into a cryo-EM density | |||||||||
Components | Maltoporin | |||||||||
Keywords | MEMBRANE PROTEIN / maltoporin / density fit / automated refinement / cryo-em | |||||||||
Function / homology | Function and homology information maltodextrin transmembrane transporter activity / maltose transporting porin activity / pore complex / monoatomic ion transport / cell outer membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Yvonnesdotter, L. / Rovsnik, U. / Blau, C. / Lycksell, M. / Howard, R.J. / Lindahl, E. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Biophys J / Year: 2023 Title: Automated simulation-based membrane protein refinement into cryo-EM data. Authors: Linnea Yvonnesdotter / Urška Rovšnik / Christian Blau / Marie Lycksell / Rebecca Joy Howard / Erik Lindahl / Abstract: The resolution revolution has increasingly enabled single-particle cryogenic electron microscopy (cryo-EM) reconstructions of previously inaccessible systems, including membrane proteins-a category ...The resolution revolution has increasingly enabled single-particle cryogenic electron microscopy (cryo-EM) reconstructions of previously inaccessible systems, including membrane proteins-a category that constitutes a disproportionate share of drug targets. We present a protocol for using density-guided molecular dynamics simulations to automatically refine atomistic models into membrane protein cryo-EM maps. Using adaptive force density-guided simulations as implemented in the GROMACS molecular dynamics package, we show how automated model refinement of a membrane protein is achieved without the need to manually tune the fitting force ad hoc. We also present selection criteria to choose the best-fit model that balances stereochemistry and goodness of fit. The proposed protocol was used to refine models into a new cryo-EM density of the membrane protein maltoporin, either in a lipid bilayer or detergent micelle, and we found that results do not substantially differ from fitting in solution. Fitted structures satisfied classical model-quality metrics and improved the quality and the model-to-map correlation of the x-ray starting structure. Additionally, the density-guided fitting in combination with generalized orientation-dependent all-atom potential was used to correct the pixel-size estimation of the experimental cryo-EM density map. This work demonstrates the applicability of a straightforward automated approach to fitting membrane protein cryo-EM densities. Such computational approaches promise to facilitate rapid refinement of proteins under different conditions or with various ligands present, including targets in the highly relevant superfamily of membrane proteins. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b7v.cif.gz | 213.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b7v.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 8b7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/8b7v ftp://data.pdbj.org/pub/pdb/validation_reports/b7/8b7v | HTTPS FTP |
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-Related structure data
Related structure data | 15903MC 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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1 |
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-Components
#1: Protein | Mass: 47425.785 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A2X5NX10 |
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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: Trimeric maltoporin (LamB protein) / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 3 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 FIELDBright-field microscopy / Nominal defocus max: 2800 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 579000 / Symmetry type: POINT |