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- PDB-9vds: Crystal structure of voltage-gated sodium channel NavAb N49K/L176... -

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Basic information

Entry
Database: PDB / ID: 9vds
TitleCrystal structure of voltage-gated sodium channel NavAb N49K/L176W mutant
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / ion channel
Function / homologyVoltage-gated cation channel calcium and sodium / voltage-gated sodium channel complex / voltage-gated sodium channel activity / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / metal ion binding / identical protein binding / Ion transport protein
Function and homology information
Biological speciesAliarcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4924
Polymers31,3261
Non-polymers1,1653
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)129,96716
Polymers125,3054
Non-polymers4,66212
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 area16370 Å2
ΔGint-161 kcal/mol
Surface area48040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.880, 126.880, 204.860
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

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Components

#1: Protein Ion transport protein


Mass: 31326.199 Da / Num. of mol.: 1 / Mutation: N49K/L176W
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.: 1 / 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: 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
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: 6.58 Å3/Da / Density % sol: 81.31 %
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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→30 Å / Num. obs: 9266 / % possible obs: 99.3 % / Redundancy: 54.4 % / Biso Wilson estimate: 152.5 Å2 / CC1/2: 1 / Net I/av σ(I): 26.57 / Net I/σ(I): 0.01715
Reflection shellResolution: 3.7→3.8 Å / Mean I/σ(I) obs: 4.83 / Num. unique obs: 869 / CC1/2: 0.986 / Rpim(I) all: 0.4321

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→29.91 Å / SU ML: 0.5821 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 43.8519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3389 434 4.7 %
Rwork0.3129 8798 -
obs0.3135 9232 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 163.57 Å2
Refinement stepCycle: LAST / Resolution: 3.7→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 68 0 1866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031919
X-RAY DIFFRACTIONf_angle_d0.48292613
X-RAY DIFFRACTIONf_chiral_restr0.0401324
X-RAY DIFFRACTIONf_plane_restr0.0034294
X-RAY DIFFRACTIONf_dihedral_angle_d15.4018680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.760.3605180.3578406X-RAY DIFFRACTION93.39
3.76-3.830.4605200.3321425X-RAY DIFFRACTION100
3.83-3.910.1905140.3255445X-RAY DIFFRACTION100
3.91-3.990.3422140.2876441X-RAY DIFFRACTION99.78
3.99-4.070.2799230.2795424X-RAY DIFFRACTION100
4.07-4.170.2961220.2753435X-RAY DIFFRACTION100
4.17-4.270.4240.3058438X-RAY DIFFRACTION100
4.27-4.380.3225210.3089429X-RAY DIFFRACTION100
4.39-4.510.3211200.3271436X-RAY DIFFRACTION100
4.51-4.660.3614200.3194433X-RAY DIFFRACTION100
4.66-4.820.3338280.3057425X-RAY DIFFRACTION100
4.83-5.020.3309290.2868435X-RAY DIFFRACTION99.78
5.02-5.240.3301180.3038454X-RAY DIFFRACTION100
5.24-5.520.2907230.3511420X-RAY DIFFRACTION100
5.52-5.860.2807210.2993441X-RAY DIFFRACTION100
5.86-6.310.392270.3884443X-RAY DIFFRACTION100
6.31-6.940.3777270.3844449X-RAY DIFFRACTION100
6.94-7.920.3116240.3243449X-RAY DIFFRACTION100
7.93-9.930.3241240.2364469X-RAY DIFFRACTION100
9.95-29.910.3652170.3265501X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 11.9153483443 Å / Origin y: -16.855383966 Å / Origin z: 25.8999512976 Å
111213212223313233
T1.98531160554 Å20.245109542323 Å20.0362682115216 Å2-1.8212301927 Å20.427353191408 Å2--0.65580681048 Å2
L1.11807671308 °2-0.533963274959 °2-0.405666409012 °2-2.14081245698 °21.54107442527 °2--1.93966591032 °2
S-0.918723032125 Å °-0.513195823452 Å °-0.923607366983 Å °1.25957350561 Å °0.521868324966 Å °0.0721105248086 Å °1.28468713228 Å °0.572982367263 Å °0.344235421515 Å °
Refinement TLS groupSelection details: all

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