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- PDB-9vdt: Crystal structure of voltage-gated sodium channel NavAb N49K DC23... -

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Basic information

Entry
Database: PDB / ID: 9vdt
TitleCrystal structure of voltage-gated sodium channel NavAb N49K DC230 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: 3.5 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)37,87313
Polymers31,2531
Non-polymers6,62012
Water905
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)151,49352
Polymers125,0134
Non-polymers26,48048
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 area32300 Å2
ΔGint-213 kcal/mol
Surface area65050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.755, 129.755, 200.315
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-

NA

21A-1302-

NA

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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
#4: 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

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Non-polymers , 4 types, 16 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / 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
#5: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 6.74 Å3/Da / Density % sol: 81.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 7%-9% PEG 6000, 100mM sodium chloride, 100mM magnesium nitrate, 100mM cadmium chloride, 10mM copper chloride, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→29.7 Å / Num. obs: 11127 / % possible obs: 98.75 % / Redundancy: 26.1 % / Biso Wilson estimate: 97.64 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.01678 / Net I/σ(I): 27.92
Reflection shellResolution: 3.5→3.6 Å / Mean I/σ(I) obs: 3.01 / Num. unique obs: 980 / CC1/2: 0.979 / Rpim(I) all: 0.2434

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→29.69 Å / SU ML: 0.4536 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.8932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3444 539 4.89 %
Rwork0.3084 10480 -
obs0.3099 11019 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.84 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 436 5 2225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282262
X-RAY DIFFRACTIONf_angle_d0.76933013
X-RAY DIFFRACTIONf_chiral_restr0.044339
X-RAY DIFFRACTIONf_plane_restr0.005308
X-RAY DIFFRACTIONf_dihedral_angle_d17.3964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.560.3137240.2839444X-RAY DIFFRACTION86.51
3.56-3.620.3064260.2638486X-RAY DIFFRACTION94.46
3.63-3.690.2231220.2669517X-RAY DIFFRACTION99.63
3.69-3.770.2216300.2537514X-RAY DIFFRACTION100
3.77-3.850.2909230.2571526X-RAY DIFFRACTION100
3.85-3.940.3101400.2717491X-RAY DIFFRACTION100
3.94-4.040.3058290.2685522X-RAY DIFFRACTION100
4.04-4.150.305310.2622520X-RAY DIFFRACTION100
4.15-4.270.3884260.2769529X-RAY DIFFRACTION100
4.27-4.410.2952260.2488516X-RAY DIFFRACTION100
4.41-4.560.2628280.2761525X-RAY DIFFRACTION100
4.56-4.750.3541250.2788525X-RAY DIFFRACTION100
4.75-4.960.3254280.2881529X-RAY DIFFRACTION100
4.96-5.220.3747350.3136529X-RAY DIFFRACTION100
5.22-5.540.3351250.3171521X-RAY DIFFRACTION100
5.55-5.970.402260.3648542X-RAY DIFFRACTION100
5.97-6.560.3736260.4358533X-RAY DIFFRACTION100
6.57-7.50.3803250.3736552X-RAY DIFFRACTION100
7.5-9.40.3447220.3051558X-RAY DIFFRACTION100
9.41-29.690.4761220.34601X-RAY DIFFRACTION99.2
Refinement TLS params.Method: refined / Origin x: 12.03135661 Å / Origin y: -16.8431516819 Å / Origin z: 25.1418936668 Å
111213212223313233
T0.995822962269 Å20.204373851189 Å2-0.135031139625 Å2-0.90440143772 Å20.408425251972 Å2--0.793469086404 Å2
L6.8132521168 °2-2.92130073982 °21.35047912293 °2-4.27255203735 °2-1.19660234281 °2--3.6829488026 °2
S-0.757633799598 Å °-1.22917251371 Å °-0.407280997353 Å °1.11057375293 Å °0.0755998347717 Å °-0.851091578706 Å °0.691621788789 Å °0.754022621102 Å °0.413268217792 Å °
Refinement TLS groupSelection details: all

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