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- PDB-5yub: Crystal structure of voltage-gated sodium channel NavAb E32Q mutant -

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Basic information

Entry
Database: PDB / ID: 5yub
TitleCrystal structure of voltage-gated sodium channel NavAb E32Q mutant
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ion transport protein / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.40003993335 Å
AuthorsIrie, K. / Shimomura, T. / Fujiyoshi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Toyoaki Scholarship Foundation Japan
CitationJournal: FEBS Lett. / Year: 2017
Title: Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb.
Authors: Irie, K. / Haga, Y. / Shimomura, T. / Fujiyoshi, Y.
History
DepositionNov 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5644
Polymers31,3811
Non-polymers1,1833
Water00
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,25516
Polymers125,5254
Non-polymers4,73012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area19680 Å2
ΔGint-201 kcal/mol
Surface area45920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.040, 127.040, 202.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1301-

CA

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Components

#1: Protein Ion transport protein / oltage gated sodium channel


Mass: 31381.221 Da / Num. of mol.: 1 / Mutation: E32Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Gene: SAMEA4475700_01771 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A239WB15, UniProt: A8EVM5*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-1N7 / CHAPSO / 2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium


Mass: 631.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H59N2O8S / Comment: detergent*YM

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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: 6.51 Å3/Da / Density % sol: 81.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% polyethylene glycol monomethyl ether 2000, 100 mM NaCl, 100 mM calcium nitrate, 100 mM Tris-HCl, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→41.07 Å / Num. obs: 11773 / % possible obs: 86.42 % / Redundancy: 13.9 % / Biso Wilson estimate: 25.3055302345 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.0689 / Net I/σ(I): 14.86
Reflection shellResolution: 3.4→3.521 Å / Rmerge(I) obs: 1.924 / CC1/2: 0.845 / Rpim(I) all: 0.543

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Processing

Software
NameVersionClassification
phenix.refine1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YUA

5yua


Resolution: 3.40003993335→41.0616138222 Å / SU ML: 0.287523667776 / Cross valid method: FREE R-VALUE / σ(F): 1.3777448541 / Phase error: 29.4465945713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.272842668034 1020 9.99901970395 %
Rwork0.240571490498 9181 -
obs0.243872770287 10201 86.5151386651 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.1650526251 Å2
Refinement stepCycle: LAST / Resolution: 3.40003993335→41.0616138222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 66 0 1931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01126298421621985
X-RAY DIFFRACTIONf_angle_d1.171234428562705
X-RAY DIFFRACTIONf_chiral_restr0.0650960318249335
X-RAY DIFFRACTIONf_plane_restr0.00622383553357310
X-RAY DIFFRACTIONf_dihedral_angle_d19.0231374819703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.57920.299577179815420.236404538484388X-RAY DIFFRACTION26.2515262515
3.5792-3.80330.2751103178961310.22810234921182X-RAY DIFFRACTION79.8176291793
3.8033-4.09670.2653188752371670.227844915791498X-RAY DIFFRACTION99.8201438849
4.0967-4.50850.2520900452421670.2257979069081495X-RAY DIFFRACTION99.8198198198
4.5085-5.15980.2470189171011660.2136745698941498X-RAY DIFFRACTION99.9399399399
5.1598-6.49670.2993018581991700.2968058810391533X-RAY DIFFRACTION99.941314554
6.4967-41.06460.298169148111770.2634449445991587X-RAY DIFFRACTION98.0544747082
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23893431047-0.3317214164040.8083317880975.72169545972-3.934355672813.583268724520.1277803909240.132657882014-0.41246588728-0.220697818248-0.112912618579-0.5849064289841.181202598660.9108013784620.01428875222720.7623629320120.435854354489-0.1662443216980.8984508421830.0462897942080.66188616728630.4986227438-22.886388859827.8719137043
23.62909224038-0.1788958281290.3631718285022.37951680019-0.8034080251681.74058448708-0.105856403815-0.520837227969-0.02870131258020.332704236216-0.06819135789550.05392387029650.17834506439-0.2502422401280.1111100306460.38637607374-0.08294231263690.09898717733060.3075104541680.04642872944150.230925685382-5.07514411156-12.200523632423.3516485536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 999 through 1112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1113 through 1227 )

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