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

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Basic information

Entry
Database: PDB / ID: 6vrr
TitleCrystal structure of a disease mutant of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain
ComponentsSodium channel subunit beta-2
KeywordsMEMBRANE PROTEIN / Sodium Channel / Beta sub-unit / SCN2B
Function / homology
Function and homology information


response to pyrethroid / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated sodium channel complex / membrane depolarization during cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / Interaction between L1 and Ankyrins / regulation of heart rate by cardiac conduction ...response to pyrethroid / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated sodium channel complex / membrane depolarization during cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / Interaction between L1 and Ankyrins / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / sodium ion transmembrane transport / sodium channel regulator activity / cardiac muscle contraction / T-tubule / Sensory perception of sweet, bitter, and umami (glutamate) taste / gene expression / nervous system development / response to heat / chemical synaptic transmission / synapse / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 9, 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-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9533
Polymers14,7691
Non-polymers1842
Water2,990166
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.271, 53.582, 59.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sodium channel subunit beta-2 /


Mass: 14768.657 Da / Num. of mol.: 1 / Mutation: R137H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN2B, UNQ326/PRO386 / Production host: Escherichia coli (E. coli) / References: UniProt: O60939
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES (pH 7.0), 14% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→40.3 Å / Num. obs: 43929 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.93 / Rrim(I) all: 0.043 / Net I/σ(I): 24.4
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 6.54 % / Mean I/σ(I) obs: 2.75 / Num. unique obs: 2827 / Rrim(I) all: 0.63 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FEB

5feb


Resolution: 1.45→39.76 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1827 2220 5.05 %
Rwork0.1499 41706 -
obs0.1516 43926 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.41 Å2 / Biso mean: 24.5613 Å2 / Biso min: 11.96 Å2
Refinement stepCycle: final / Resolution: 1.45→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 28 166 1226
Biso mean--42.4 33.84 -
Num. residues----127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.45-1.480.3021340.306226072741
1.48-1.520.24711150.238326262741
1.52-1.550.22911870.177425332720
1.55-1.60.16591410.15926252766
1.6-1.640.18241310.1526242755
1.64-1.70.20171250.148626082733
1.7-1.760.18831470.154226012748
1.76-1.830.16261360.134826112747
1.83-1.910.16441390.137226182757
1.91-2.010.17361260.129525992725
2.01-2.140.15941380.127326252763
2.14-2.30.1541480.138525892737
2.3-2.530.17651340.146326252759
2.53-2.90.20081660.149625722738
2.9-3.650.16141170.146826332750
3.65-39.760.20351360.158926102746

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