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- PDB-7x5v: NaVEh Sodium channel, and NaVEh from the coccolithophore Emiliani... -

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Basic information

Entry
Database: PDB / ID: 7x5v
TitleNaVEh Sodium channel, and NaVEh from the coccolithophore Emiliania huxleyi
Components
  • ion channel
  • ion channel,GFP-TwinStrep
KeywordsTRANSPORT PROTEIN / ion channel
Biological speciesEmiliania huxleyi (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsJiang, D. / Zhang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Nat Commun / Year: 2022
Title: N-type fast inactivation of a eukaryotic voltage-gated sodium channel.
Authors: Jiangtao Zhang / Yiqiang Shi / Junping Fan / Huiwen Chen / Zhanyi Xia / Bo Huang / Juquan Jiang / Jianke Gong / Zhuo Huang / Daohua Jiang /
Abstract: Voltage-gated sodium (Na) channels initiate action potentials. Fast inactivation of Na channels, mediated by an Ile-Phe-Met motif, is crucial for preventing hyperexcitability and regulating firing ...Voltage-gated sodium (Na) channels initiate action potentials. Fast inactivation of Na channels, mediated by an Ile-Phe-Met motif, is crucial for preventing hyperexcitability and regulating firing frequency. Here we present cryo-electron microscopy structure of NaEh from the coccolithophore Emiliania huxleyi, which reveals an unexpected molecular gating mechanism for Na channel fast inactivation independent of the Ile-Phe-Met motif. An N-terminal helix of NaEh plugs into the open activation gate and blocks it. The binding pose of the helix is stabilized by multiple electrostatic interactions. Deletion of the helix or mutations blocking the electrostatic interactions completely abolished the fast inactivation. These strong interactions enable rapid inactivation, but also delay recovery from fast inactivation, which is ~160-fold slower than human Na channels. Together, our results provide mechanistic insights into fast inactivation of NaEh that fundamentally differs from the conventional local allosteric inhibition, revealing both surprising structural diversity and functional conservation of ion channel inactivation.
History
DepositionMar 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ion channel,GFP-TwinStrep
B: ion channel,GFP-TwinStrep
C: ion channel,GFP-TwinStrep
D: ion channel,GFP-TwinStrep
E: ion channel


Theoretical massNumber of molelcules
Total (without water)368,6515
Polymers368,6515
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ion channel,GFP-TwinStrep


Mass: 91684.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emiliania huxleyi (eukaryote) / Production host: Homo sapiens (human)
#2: Protein/peptide ion channel


Mass: 1913.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal helix of either of the four protomers / Source: (gene. exp.) Emiliania huxleyi (eukaryote) / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ion channel complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Emiliania huxleyi (eukaryote)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61065 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069612
ELECTRON MICROSCOPYf_angle_d0.66913072
ELECTRON MICROSCOPYf_dihedral_angle_d5.4181272
ELECTRON MICROSCOPYf_chiral_restr0.0431440
ELECTRON MICROSCOPYf_plane_restr0.0051632

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