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- PDB-6vsv: Crystal structure of a disease mutant of the Voltage-gated Sodium... -

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Basic information

Entry
Database: PDB / ID: 6vsv
TitleCrystal structure of a disease mutant of the Voltage-gated Sodium Channel Beta 4 subunit extracellular domain
ComponentsSodium channel subunit beta-4
KeywordsMEMBRANE PROTEIN / Sodium Channel / Beta4 subunit / Disease mutant
Function / homology
Function and homology information


AV node cell action potential / regulation of sodium ion transmembrane transporter activity / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / regulation of ventricular cardiac muscle cell membrane repolarization / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity ...AV node cell action potential / regulation of sodium ion transmembrane transporter activity / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / regulation of ventricular cardiac muscle cell membrane repolarization / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / intercalated disc / sodium channel regulator activity / sodium ion transmembrane transport / neuronal action potential / cardiac muscle contraction / establishment of localization in cell / Sensory perception of sweet, bitter, and umami (glutamate) taste / transmembrane transporter binding / plasma membrane
Similarity search - Function
Myelin P0 protein-related / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sodium channel subunit beta-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDas, S. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Bioelectricity / Year: 2020
Title: Biophysical Investigation of Sodium Channel Interaction with beta-Subunit Variants Associated with Arrhythmias.
Authors: Llongueras, J.P. / Das, S. / De Waele, J. / Capulzini, L. / Sorgente, A. / Van Petegem, F. / Bosmans, F.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium channel subunit beta-4


Theoretical massNumber of molelcules
Total (without water)14,5611
Polymers14,5611
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.123, 43.123, 107.492
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Sodium channel subunit beta-4 /


Mass: 14561.279 Da / Num. of mol.: 1 / Mutation: I80T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN4B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IWT1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 (M) MES, pH 6.5, 15-17% PEG200-MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 15397 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rrim(I) all: 0.079 / Net I/σ(I): 33.5
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 983 / Rrim(I) all: 0.65 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MZ2

4mz2


Resolution: 1.62→37.346 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.23
RfactorNum. reflection% reflection
Rfree0.2081 676 4.39 %
Rwork0.1847 --
obs0.1857 15397 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.54 Å2 / Biso mean: 35.551 Å2 / Biso min: 15.11 Å2
Refinement stepCycle: final / Resolution: 1.62→37.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 0 147 1058
Biso mean---48.43 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121021
X-RAY DIFFRACTIONf_angle_d1.2291399
X-RAY DIFFRACTIONf_chiral_restr0.081163
X-RAY DIFFRACTIONf_plane_restr0.008180
X-RAY DIFFRACTIONf_dihedral_angle_d3.446812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.62-1.74510.24991430.22912862
1.7451-1.92070.23811350.20742889
1.9207-2.19860.22021190.19312927
2.1986-2.76990.24131410.20432935
Refinement TLS params.Method: refined / Origin x: -9.4792 Å / Origin y: 18.9772 Å / Origin z: 4.2786 Å
111213212223313233
T0.1113 Å2-0.016 Å2-0.0144 Å2-0.1145 Å20.014 Å2--0.1395 Å2
L3.0334 °20.1889 °2-1.7633 °2-3.0769 °20.4874 °2--4.6711 °2
S0.0217 Å °-0.0437 Å °-0.0552 Å °0.087 Å °-0.0115 Å °0.0641 Å °-0.0172 Å °-0.0771 Å °0.0076 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA37 - 154
2X-RAY DIFFRACTION1allS1 - 160

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