[English] 日本語
Yorodumi- PDB-5vb8: Crystal structure of the NavAb voltage-gated sodium channel in an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vb8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the NavAb voltage-gated sodium channel in an open state | |||||||||
Components | Ion transport proteinIon transporter | |||||||||
Keywords | TRANSPORT PROTEIN / Voltage-gated sodium channel | |||||||||
Function / homology | Function and homology information monoatomic cation channel activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Arcobacter butzleri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Lenaeus, M.J. / Catterall, W.A. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structures of closed and open states of a voltage-gated sodium channel. Authors: Lenaeus, M.J. / Gamal El-Din, T.M. / Ing, C. / Ramanadane, K. / Pomes, R. / Zheng, N. / Catterall, W.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5vb8.cif.gz | 144 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5vb8.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/5vb8 ftp://data.pdbj.org/pub/pdb/validation_reports/vb/5vb8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5vb2C 3rvyS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 28202.602 Da / Num. of mol.: 1 / Fragment: UNP residues 1-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (bacteria) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | ChemComp-PX4 / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 6.7 Å3/Da / Density % sol: 81.63 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 1.8 M ammonium sulfate and 100 mM sodium acetate (pH 4.8). 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC):CHAPSO bicelles (Anatrace) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→29.53 Å / Num. obs: 16684 / % possible obs: 91.13 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.85→2.9 Å / CC1/2: 0.51 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RVY Resolution: 2.85→29.53 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.54
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→29.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|