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Yorodumi- PDB-6p6y: Crystal structure of voltage-gated sodium channel NavAb V100C/Q15... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p6y | |||||||||||||||
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Title | Crystal structure of voltage-gated sodium channel NavAb V100C/Q150C disulfide crosslinked mutant in the activated state | |||||||||||||||
Components | Ion transport protein | |||||||||||||||
Keywords | membrane protein / metal transport / Ion 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 | Arcobacter butzleri (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | |||||||||||||||
Authors | Wisedchaisri, G. / Tonggu, L. / McCord, E. / Gamal El-din, T.M. / Wang, L. / Zheng, N. / Catterall, W.A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Cell / Year: 2019 Title: Resting-State Structure and Gating Mechanism of a Voltage-Gated Sodium Channel. Authors: Goragot Wisedchaisri / Lige Tonggu / Eedann McCord / Tamer M Gamal El-Din / Liguo Wang / Ning Zheng / William A Catterall / Abstract: Voltage-gated sodium (Na) channels initiate action potentials in nerve, muscle, and other electrically excitable cells. The structural basis of voltage gating is uncertain because the resting state ...Voltage-gated sodium (Na) channels initiate action potentials in nerve, muscle, and other electrically excitable cells. The structural basis of voltage gating is uncertain because the resting state exists only at deeply negative membrane potentials. To stabilize the resting conformation, we inserted voltage-shifting mutations and introduced a disulfide crosslink in the VS of the ancestral bacterial sodium channel NaAb. Here, we present a cryo-EM structure of the resting state and a complete voltage-dependent gating mechanism. The S4 segment of the VS is drawn intracellularly, with three gating charges passing through the transmembrane electric field. This movement forms an elbow connecting S4 to the S4-S5 linker, tightens the collar around the S6 activation gate, and prevents its opening. Our structure supports the classical "sliding helix" mechanism of voltage sensing and provides a complete gating mechanism for voltage sensor function, pore opening, and activation-gate closure based on high-resolution structures of a single sodium channel protein. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p6y.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p6y.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 6p6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p6y_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 6p6y_full_validation.pdf.gz | 465 KB | Display | |
Data in XML | 6p6y_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 6p6y_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/6p6y ftp://data.pdbj.org/pub/pdb/validation_reports/p6/6p6y | HTTPS FTP |
-Related structure data
Related structure data | 6p6wC 6p6xC 3rvyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29768.320 Da / Num. of mol.: 1 / Mutation: V100C, Q150C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria) Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5 | ||||
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#2: Chemical | #3: 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: 6.29 Å3/Da / Density % sol: 80.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.8 M ammonium sulfate 0.1 M sodium citrate pH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K / 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: Jul 29, 2016 |
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: 2.89→50 Å / Num. obs: 16988 / % possible obs: 97.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 54.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.035 / Rrim(I) all: 0.13 / Χ2: 1.125 / Net I/σ(I): 22.06 |
Reflection shell | Resolution: 2.89→2.94 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 638 / CC1/2: 0.831 / Rpim(I) all: 0.253 / Rrim(I) all: 0.703 / Χ2: 0.755 / % possible all: 76.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RVY Resolution: 2.89→44.53 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.046 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.3 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.234 Å2
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Refinement step | Cycle: 1 / Resolution: 2.89→44.53 Å
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Refine LS restraints |
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