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- PDB-9vdq: Crystal structure of voltage-gated sodium channel NavAb N49K mutant -

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Basic information

Entry
Database: PDB / ID: 9vdq
TitleCrystal structure of voltage-gated sodium channel NavAb N49K 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 cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesAliarcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsIrie, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K17795 Japan
Japan Society for the Promotion of Science (JSPS)20K09193 Japan
Japan Society for the Promotion of Science (JSPS)24K02168 Japan
CitationJournal: Biorxiv / Year: 2025
Title: Conformational dynamics underlying slow inactivation in voltage-gated sodium channels.
Authors: Irie, K. / Han, S. / Applewhite, S. / Maeda, Y.K. / Vance, J. / Wang, S.
History
DepositionJun 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,38613
Polymers31,2531
Non-polymers6,13212
Water18010
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)149,54252
Polymers125,0134
Non-polymers24,52948
Water724
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 area41060 Å2
ΔGint-175 kcal/mol
Surface area54340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.183, 127.183, 201.410
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-1302-

NA

21A-1407-

HOH

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Components

#1: Protein Ion transport protein


Mass: 31253.148 Da / Num. of mol.: 1 / Mutation: N49K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliarcobacter butzleri (strain RM4018) (bacteria)
Gene: Abu_1752 / Production host: Escherichia coli (E. coli) / References: UniProt: A8EVM5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 6.52 Å3/Da / Density % sol: 81.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Nov 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→43.93 Å / Num. obs: 15361 / % possible obs: 96.15 % / Redundancy: 14.6 % / Biso Wilson estimate: 65.66 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03479 / Net I/σ(I): 21.38
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 1.95 / Num. unique obs: 1079 / CC1/2: 0.886 / Rpim(I) all: 0.4332

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→43.93 Å / SU ML: 0.3909 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2893 1480 10 %
Rwork0.2412 13327 -
obs0.2457 14807 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.96 Å2
Refinement stepCycle: LAST / Resolution: 3.1→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 401 10 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112314
X-RAY DIFFRACTIONf_angle_d1.45283086
X-RAY DIFFRACTIONf_chiral_restr0.0752341
X-RAY DIFFRACTIONf_plane_restr0.0081325
X-RAY DIFFRACTIONf_dihedral_angle_d25.0666986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.150.3375490.307451X-RAY DIFFRACTION66.14
3.15-3.210.3546580.2783521X-RAY DIFFRACTION75.98
3.21-3.270.314660.2825592X-RAY DIFFRACTION88.32
3.27-3.340.2923730.2616653X-RAY DIFFRACTION97.32
3.34-3.410.2558750.2473680X-RAY DIFFRACTION99.74
3.41-3.490.2798750.2439678X-RAY DIFFRACTION100
3.49-3.580.2631740.2254672X-RAY DIFFRACTION100
3.58-3.680.2959770.1991689X-RAY DIFFRACTION100
3.68-3.780.2356760.2055678X-RAY DIFFRACTION100
3.78-3.90.2821760.219687X-RAY DIFFRACTION100
3.91-4.050.2649770.2163685X-RAY DIFFRACTION100
4.05-4.210.2842760.2274686X-RAY DIFFRACTION100
4.21-4.40.3193770.226690X-RAY DIFFRACTION100
4.4-4.630.2377760.206688X-RAY DIFFRACTION99.74
4.63-4.920.2971770.2174698X-RAY DIFFRACTION100
4.92-5.30.2819780.2235702X-RAY DIFFRACTION100
5.3-5.830.3136780.2602698X-RAY DIFFRACTION100
5.83-6.670.2802790.3209708X-RAY DIFFRACTION100
6.67-8.390.255790.2795720X-RAY DIFFRACTION100
8.4-43.930.3616840.2616751X-RAY DIFFRACTION96.42
Refinement TLS params.Method: refined / Origin x: 11.6638262041 Å / Origin y: -16.8019396884 Å / Origin z: 25.6958802406 Å
111213212223313233
T0.56062976921 Å20.135296262475 Å2-0.0452802319928 Å2-0.342310078506 Å20.145328313577 Å2--0.408537663492 Å2
L4.29109366355 °2-0.6253578021 °21.33707889098 °2-1.54070339441 °2-0.106395843592 °2--3.02418915818 °2
S0.0343255716578 Å °-0.283903364977 Å °-0.331818624802 Å °0.403220866576 Å °-0.0940389873719 Å °-0.397973150002 Å °0.797478268219 Å °0.540717700169 Å °0.0553414565671 Å °
Refinement TLS groupSelection details: all

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