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- PDB-5xaw: Parallel homodimer structures of voltage-gated sodium channel bet... -

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Basic information

Entry
Database: PDB / ID: 5xaw
TitleParallel homodimer structures of voltage-gated sodium channel beta4 for 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 / 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 / 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 / regulation of ventricular cardiac muscle cell membrane repolarization / voltage-gated sodium channel complex / 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 ion transmembrane transport / sodium channel regulator activity / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)29,1999
Polymers27,7792
Non-polymers1,4207
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-21 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.079, 57.079, 72.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Sodium channel subunit beta-4


Mass: 13889.707 Da / Num. of mol.: 2 / Fragment: UNP residues 30-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN4B / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q8IWT1
#2: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 10% (w/v) PEG1000, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.107 Å / Num. obs: 14834 / % possible obs: 97.4 % / Redundancy: 6.4 % / Net I/σ(I): 32.5

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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: 2.101→29.107 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1483 10 %
Rwork0.2043 --
obs0.2102 14834 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→29.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 95 41 1901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071885
X-RAY DIFFRACTIONf_angle_d0.9642516
X-RAY DIFFRACTIONf_dihedral_angle_d9.1951114
X-RAY DIFFRACTIONf_chiral_restr0.056289
X-RAY DIFFRACTIONf_plane_restr0.006305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1011-2.16890.34981050.2453940X-RAY DIFFRACTION76
2.1689-2.24630.25261360.24481179X-RAY DIFFRACTION92
2.2463-2.33620.3091310.22111221X-RAY DIFFRACTION99
2.3362-2.44250.2261430.20891257X-RAY DIFFRACTION100
2.4425-2.57120.32751400.21281259X-RAY DIFFRACTION100
2.5712-2.73220.29071380.21531247X-RAY DIFFRACTION100
2.7322-2.9430.24741340.2191241X-RAY DIFFRACTION100
2.943-3.23880.26591380.21431255X-RAY DIFFRACTION100
3.2388-3.70660.23721460.18941248X-RAY DIFFRACTION100
3.7066-4.66690.26971320.18581262X-RAY DIFFRACTION100
4.6669-29.10970.26011400.20781242X-RAY DIFFRACTION99

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