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Yorodumi- PDB-8div: Crystal structure of NavAb I22V as a basis for the human Nav1.7 I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8div | |||||||||||||||
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Title | Crystal structure of NavAb I22V as a basis for the human Nav1.7 Inherited Erythromelalgia I136V mutation | |||||||||||||||
Components | Ion transport protein | |||||||||||||||
Keywords | MEMBRANE PROTEIN / Voltage-gated sodium channel Ion transport protein | |||||||||||||||
Function / homology | Function and homology information membrane depolarization during action potential / voltage-gated sodium channel complex / voltage-gated sodium channel activity / identical protein binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Aliarcobacter butzleri RM4018 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | |||||||||||||||
Authors | Wisedchaisri, G. / Gamal El-Din, T.M. / Powell, N.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 | 8div.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8div.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 8div.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8div_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8div_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8div_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 8div_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/8div ftp://data.pdbj.org/pub/pdb/validation_reports/di/8div | HTTPS FTP |
-Related structure data
Related structure data | 8diwC 8dixC 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: 29775.270 Da / Num. of mol.: 1 / Mutation: I22V 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: Sugar | ChemComp-BGC / | ||||||
#3: Chemical | ChemComp-PX4 / #4: Chemical | #5: Water | ChemComp-HOH / | 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: 6.22 Å3/Da / Density % sol: 80.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.7-1.8 M Ammonium sulfate 0.1 M Sodium Citrate pH 5.0 |
-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: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2009 |
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: 2.53→50 Å / Num. obs: 22384 / % possible obs: 87.6 % / Redundancy: 11.5 % / Biso Wilson estimate: 37.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.045 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.53→2.57 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 0.43 / Num. unique obs: 415 / CC1/2: 0.886 / Rpim(I) all: 0.36 / % possible all: 33.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RVY Resolution: 2.54→41.97 Å / SU ML: 0.2531 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4922 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: 48.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→41.97 Å
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Refine LS restraints |
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LS refinement shell |
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