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Yorodumi- PDB-8dix: Structure of NavAb L98R as a basis for the human Nav1.7 Inherited... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dix | |||||||||||||||
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Title | Structure of NavAb L98R as a basis for the human Nav1.7 Inherited Erythromelalgia L823R mutation | |||||||||||||||
Components | Ion transport proteinIon transporter | |||||||||||||||
Keywords | MEMBRANE PROTEIN / Voltage-gated sodium channel Ion transport protein | |||||||||||||||
Function / homology | Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / monoatomic cation channel activity / Ion transport domain / Ion transport protein / identical protein binding / plasma membrane / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein Function and homology information | |||||||||||||||
Biological species | Aliarcobacter butzleri RM4018 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||||||||
Authors | Wisedchaisri, G. / Gamal El-Din, T.M. / Zheng, N. / Catterall, W.A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J.Gen.Physiol. / Year: 2023 Title: Structural basis for severe pain caused by mutations in the voltage sensors of sodium channel NaV1.7. Authors: Wisedchaisri, G. / Gamal El-Din, T.M. / Powell, N.M. / Zheng, N. / Catterall, W.A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dix.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dix.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 8dix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/8dix ftp://data.pdbj.org/pub/pdb/validation_reports/di/8dix | HTTPS FTP |
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-Related structure data
Related structure data | 8divC 8diwC 8diyC 3rvyS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 29833.328 Da / Num. of mol.: 1 / Mutation: L98R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aliarcobacter butzleri RM4018 (bacteria) Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5 | ||
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#2: Chemical | ChemComp-PX4 / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.41 Å3/Da / Density % sol: 80.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 1.8-1.9 M Ammonium Sulfate 0.1 M Sodium Citrate pH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2019 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 11997 / % possible obs: 99.4 % / Redundancy: 11 % / Biso Wilson estimate: 43.93 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.062 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.379 / Num. unique obs: 542 / CC1/2: 0.526 / Rpim(I) all: 0.516 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RVY Resolution: 3.3→44.57 Å / SU ML: 0.4233 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.2886 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.26 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→44.57 Å
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Refine LS restraints |
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LS refinement shell |
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