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- PDB-4x89: NavMs voltage-gated sodium channal pore and C-terminal domain soa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x89 | |||||||||
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Title | NavMs voltage-gated sodium channal pore and C-terminal domain soaked with Silver nitrate | |||||||||
![]() | Ion transport protein | |||||||||
![]() | TRANSPORT PROTEIN / SELECTIVITY FILTER / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() membrane depolarization during action potential / voltage-gated sodium channel complex / voltage-gated sodium channel activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Naylor, C.E. / Bagneris, C. / Wallace, B.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of ion permeability in a voltage-gated sodium channel. Authors: Naylor, C.E. / Bagneris, C. / DeCaen, P.G. / Sula, A. / Scaglione, A. / Clapham, D.E. / Wallace, B.A. #1: ![]() Title: Role of the C-terminal domain in the structure and function of tetrameric sodium channels. Authors: Bagneris, C. / Decaen, P.G. / Hall, B.A. / Naylor, C.E. / Clapham, D.E. / Kay, C.W. / Wallace, B.A. #2: ![]() Title: Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing. Authors: McCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.5 KB | Display | ![]() |
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PDB format | ![]() | 135.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4x88C ![]() 4x8aC ![]() 5bzbC ![]() 3zjzS ![]() 4x87 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 16836.502 Da / Num. of mol.: 4 Fragment: NavMS pore and C-terminal domain, UNP residues 130-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 283 molecules ![](data/chem/img/2CV.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/AG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/AG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-2CV / #3: Chemical | ChemComp-1PE / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-AG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.43 Å3/Da / Density % sol: 83.5 % / Description: Flat plates |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M NA3CITRATE, 0.1 M TRIS, PH 8.0, 34% PEG400 / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→45.31 Å / Num. all: 32401 / Num. obs: 32142 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 52.94 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.62→2.74 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.7 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZJZ Resolution: 2.62→45.25 Å / Cor.coef. Fo:Fc: 0.8794 / Cor.coef. Fo:Fc free: 0.8885 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.204
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Displacement parameters | Biso mean: 45.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.355 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.62→45.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.71 Å / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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