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- PDB-5feb: Crystal structure of the Voltage-gated Sodium Channel Beta 2 subu... -

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Basic information

Entry
Database: PDB / ID: 5feb
TitleCrystal structure of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain
ComponentsSodium channel subunit beta-2
KeywordsMEMBRANE PROTEIN / Membrane protein Ion Channel Sodium
Function / homology
Function and homology information


response to pyrethroid / regulation of sodium ion transmembrane transporter activity / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / Phase 0 - rapid depolarisation ...response to pyrethroid / regulation of sodium ion transmembrane transporter activity / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / sodium ion transmembrane transport / sodium channel regulator activity / cardiac muscle contraction / T-tubule / Sensory perception of sweet, bitter, and umami (glutamate) taste / nervous system development / gene expression / 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 / Immunoglobulins / Immunoglobulin-like fold ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sodium channel subunit beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsDas, S. / Van Petegem, F.
CitationJournal: Elife / Year: 2016
Title: Binary architecture of the Nav1.2-beta 2 signaling complex.
Authors: Das, S. / Gilchrist, J. / Bosmans, F. / Van Petegem, F.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,6542
Polymers14,5611
Non-polymers921
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.700, 59.420, 71.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sodium channel subunit beta-2


Mass: 14561.475 Da / Num. of mol.: 1 / Fragment: UNP residues 30-151 / Mutation: C55A
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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2014
RadiationMonochromator: Double Crystal Monochromator with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.17→45.67 Å / Num. obs: 39170 / % possible obs: 99.4 % / Redundancy: 14.08 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.36
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.933 / Mean I/σ(I) obs: 1.81 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FDY

5fdy


Resolution: 1.35→45.636 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 1378 5 %
Rwork0.1722 --
obs0.1738 27540 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→45.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 6 119 1114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091267
X-RAY DIFFRACTIONf_angle_d0.9951753
X-RAY DIFFRACTIONf_dihedral_angle_d18.473519
X-RAY DIFFRACTIONf_chiral_restr0.082183
X-RAY DIFFRACTIONf_plane_restr0.005240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.39830.40141350.33622555X-RAY DIFFRACTION100
1.3983-1.45420.31241360.26482589X-RAY DIFFRACTION100
1.4542-1.52040.24181350.21222561X-RAY DIFFRACTION100
1.5204-1.60060.22151370.17562601X-RAY DIFFRACTION100
1.6006-1.70090.23411360.16992584X-RAY DIFFRACTION100
1.7009-1.83220.23561360.16372587X-RAY DIFFRACTION100
1.8322-2.01660.20091370.14872608X-RAY DIFFRACTION100
2.0166-2.30840.21211380.15092621X-RAY DIFFRACTION100
2.3084-2.90830.18371400.17222658X-RAY DIFFRACTION100
2.9083-45.66220.18671480.16682797X-RAY DIFFRACTION100

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