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- PDB-5xax: Parallel homodimer structures of the extracellular domains of the... -

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Basic information

Entry
Database: PDB / ID: 5xax
TitleParallel homodimer structures of the extracellular domains of the voltage-gated sodium channel beta4 subunit explain its role in cell-cell adhesion
ComponentsSodium channel subunit beta-4
KeywordsCELL ADHESION / Ig
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 / voltage-gated monoatomic ion channel activity / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / voltage-gated sodium channel complex / 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 / voltage-gated monoatomic ion channel activity / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / voltage-gated sodium channel complex / voltage-gated sodium channel activity / sodium ion transport / regulation of heart rate by cardiac conduction / intercalated disc / sodium ion transmembrane transport / sodium channel regulator activity / cardiac muscle contraction / establishment of localization in cell / 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 / 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-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsShimizu, H. / Yokoyama, S.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel beta 4 subunit explain its role in cell-cell adhesion
Authors: Shimizu, H. / Tosaki, A. / Ohsawa, N. / Ishizuka-Katsura, Y. / Shoji, S. / Miyazaki, H. / Oyama, F. / Terada, T. / Shirouzu, M. / Sekine, S.I. / Nukina, N. / Yokoyama, S.
History
DepositionMar 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 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-4
B: Sodium channel subunit beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6753
Polymers31,5832
Non-polymers921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-19 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.545, 131.545, 131.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Sodium channel subunit beta-4


Mass: 15791.683 Da / Num. of mol.: 2 / Fragment: Extracellula domain, UNP residues 30-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Scn4b, Gm1471
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q7M729
#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

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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: 3 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.7M Na-malonate, 0.1M Tris-HCl (pH 7.0), 0.5 % (v/v) Tween 20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.8 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.9→35.2 Å / Num. obs: 8526 / % possible obs: 99.6 % / Redundancy: 7.8 % / Net I/σ(I): 31.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AYQ

5ayq


Resolution: 2.903→35.157 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2994 853 10 %
Rwork0.2468 --
obs0.252 8526 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.903→35.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 6 0 1891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051917
X-RAY DIFFRACTIONf_angle_d0.9782590
X-RAY DIFFRACTIONf_dihedral_angle_d7.5371149
X-RAY DIFFRACTIONf_chiral_restr0.053305
X-RAY DIFFRACTIONf_plane_restr0.005327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9025-3.08430.39171420.3461267X-RAY DIFFRACTION100
3.0843-3.32220.36911390.30861272X-RAY DIFFRACTION100
3.3222-3.65620.34451390.27881267X-RAY DIFFRACTION100
3.6562-4.18460.31841400.26291273X-RAY DIFFRACTION100
4.1846-5.26930.26451440.20641288X-RAY DIFFRACTION100
5.2693-35.15940.27341490.23291306X-RAY DIFFRACTION98

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