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- PDB-4bgn: cryo-EM structure of the NavCt voltage-gated sodium channel -

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Basic information

Entry
Database: PDB / ID: 4bgn
Titlecryo-EM structure of the NavCt voltage-gated sodium channel
ComponentsVOLTAGE-GATED SODIUM CHANNELSodium channel
KeywordsTRANSPORT PROTEIN
Function / homologyVoltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / monoatomic ion channel activity / membrane / Ion transport protein
Function and homology information
Biological speciesCALDALKALIBACILLUS THERMARUM (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 9 Å
AuthorsTsai, C.J. / Tani, K. / Irie, K. / Hiroaki, Y. / Shimomura, T. / Mcmillan, D.G. / Cook, G.M. / Schertler, G. / Fujiyoshi, Y. / Li, X.D.
CitationJournal: J Mol Biol / Year: 2013
Title: Two alternative conformations of a voltage-gated sodium channel.
Authors: Ching-Ju Tsai / Kazutoshi Tani / Katsumasa Irie / Yoko Hiroaki / Takushi Shimomura / Duncan G McMillan / Gregory M Cook / Gebhard F X Schertler / Yoshinori Fujiyoshi / Xiao-Dan Li /
Abstract: Activation and inactivation of voltage-gated sodium channels (Navs) are well studied, yet the molecular mechanisms governing channel gating in the membrane remain unknown. We present two ...Activation and inactivation of voltage-gated sodium channels (Navs) are well studied, yet the molecular mechanisms governing channel gating in the membrane remain unknown. We present two conformations of a Nav from Caldalkalibacillus thermarum reconstituted into lipid bilayers in one crystal at 9Å resolution based on electron crystallography. Despite a voltage sensor arrangement identical with that in the activated form, we observed two distinct pore domain structures: a prominent form with a relatively open inner gate and a closed inner-gate conformation similar to the first prokaryotic Nav structure. Structural differences, together with mutational and electrophysiological analyses, indicated that widening of the inner gate was dependent on interactions among the S4-S5 linker, the N-terminal part of S5 and its adjoining part in S6, and on interhelical repulsion by a negatively charged C-terminal region subsequent to S6. Our findings suggest that these specific interactions result in two conformational structures.
History
DepositionMar 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation / em_image_scans / em_single_particle_entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation.pdbx_scattering_type

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  • EMDB-2347
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  • EMDB-2347
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Assembly

Deposited unit
A: VOLTAGE-GATED SODIUM CHANNEL
B: VOLTAGE-GATED SODIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)68,9542
Polymers68,9542
Non-polymers00
Water0
1
A: VOLTAGE-GATED SODIUM CHANNEL

A: VOLTAGE-GATED SODIUM CHANNEL

A: VOLTAGE-GATED SODIUM CHANNEL

A: VOLTAGE-GATED SODIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)137,9094
Polymers137,9094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation4_465y-1,-x+1,z1
2
B: VOLTAGE-GATED SODIUM CHANNEL

B: VOLTAGE-GATED SODIUM CHANNEL

B: VOLTAGE-GATED SODIUM CHANNEL

B: VOLTAGE-GATED SODIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)137,9094
Polymers137,9094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)115.000, 115.000, 118.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein VOLTAGE-GATED SODIUM CHANNEL / Sodium channel


Mass: 34477.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CALDALKALIBACILLUS THERMARUM (bacteria)
Strain: TA2.A1 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: F5L478

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: NavCt voltage-gated sodium channel / Type: COMPLEX
Buffer solutionpH: 9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA KF80 / Cryogen name: NITROGEN
Crystal growpH: 9 / Details: pH 9.0

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Data collection

MicroscopyModel: JEOL KYOTO-3000SFF / Date: Nov 5, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 40000 X / Nominal defocus max: 3820 nm / Nominal defocus min: 910 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
DiffractionMean temperature: 77 K
DetectorDate: Nov 5, 2010
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionResolution: 9→115 Å / Num. obs: 1369 / % possible obs: 76.7 % / Biso Wilson estimate: 250 Å2

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Processing

Software
NameVersionClassification
MRCmodel building
CNS1.1refinement
MRCSUITEdata scaling
MRCphasing
3D reconstructionResolution: 9 Å / Resolution method: OTHER / Symmetry type: 2D CRYSTAL
RefinementStarting model: 3RVY

3rvy


Resolution: 9→115 Å / Rfactor Rfree error: 0.058 / Data cutoff high absF: 1042112.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2347. (DEPOSITION ID: 11571).
RfactorNum. reflection% reflectionSelection details
Rfree0.473 67 4.9 %RANDOM
Rwork0.497 ---
obs0.497 1369 76.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 2.96 Å / Luzzati sigma a obs: 2.66 Å
Refinement stepCycle: LAST / Resolution: 9→115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 0 0 3464
Refine LS restraints
Refine-IDTypeDev ideal
ELECTRON CRYSTALLOGRAPHYc_bond_d0.004
ELECTRON CRYSTALLOGRAPHYc_bond_d_na
ELECTRON CRYSTALLOGRAPHYc_bond_d_prot
ELECTRON CRYSTALLOGRAPHYc_angle_d
ELECTRON CRYSTALLOGRAPHYc_angle_d_na
ELECTRON CRYSTALLOGRAPHYc_angle_d_prot
ELECTRON CRYSTALLOGRAPHYc_angle_deg1
ELECTRON CRYSTALLOGRAPHYc_angle_deg_na
ELECTRON CRYSTALLOGRAPHYc_angle_deg_prot
ELECTRON CRYSTALLOGRAPHYc_dihedral_angle_d15.6
ELECTRON CRYSTALLOGRAPHYc_dihedral_angle_d_na
ELECTRON CRYSTALLOGRAPHYc_dihedral_angle_d_prot
ELECTRON CRYSTALLOGRAPHYc_improper_angle_d0.77
ELECTRON CRYSTALLOGRAPHYc_improper_angle_d_na
ELECTRON CRYSTALLOGRAPHYc_improper_angle_d_prot
ELECTRON CRYSTALLOGRAPHYc_mcbond_it
ELECTRON CRYSTALLOGRAPHYc_mcangle_it
ELECTRON CRYSTALLOGRAPHYc_scbond_it
ELECTRON CRYSTALLOGRAPHYc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 9→9.41 Å / Rfactor Rfree error: 0.229 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.562 6 4.6 %
Rwork0.501 125 -
obs--59.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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