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- PDB-24js: Crystal structure of voltage-gated sodium channel NavAb N49K mutant -

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Basic information

Entry
Database: PDB / ID: 24js
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 RM4018 (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
DepositionMar 6, 2026Deposition 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)33,5795
Polymers31,0791
Non-polymers2,5004
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)134,31820
Polymers124,3164
Non-polymers10,00216
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 area25140 Å2
ΔGint-165 kcal/mol
Surface area46440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.850, 126.850, 203.430
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

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Components

#1: Protein Ion transport protein


Mass: 31078.996 Da / Num. of mol.: 1 / Mutation: N49K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliarcobacter butzleri RM4018 (bacteria)
Gene: Abu_1752 / Production host: Escherichia coli (E. coli) / References: UniProt: A8EVM5
#2: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*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: 6.6 Å3/Da / Density % sol: 81.37 %
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: NanoTerasu / Beamline: BL09U MX-ES / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→44.91 Å / Num. obs: 10990 / % possible obs: 96.66 % / Redundancy: 90.9 % / Biso Wilson estimate: 68.82 Å2 / CC1/2: 0.983 / Rpim(I) all: 0.07082 / Net I/σ(I): 21.15
Reflection shellResolution: 3.5→3.625 Å / Mean I/σ(I) obs: 3.11 / Num. unique obs: 803 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→28.36 Å / SU ML: 0.2954 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.0874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 524 5.21 %
Rwork0.2521 9526 -
obs0.2532 10050 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.87 Å2
Refinement stepCycle: LAST / Resolution: 3.5→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 159 0 1956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282007
X-RAY DIFFRACTIONf_angle_d0.70262716
X-RAY DIFFRACTIONf_chiral_restr0.0445329
X-RAY DIFFRACTIONf_plane_restr0.0054299
X-RAY DIFFRACTIONf_dihedral_angle_d17.3515345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.560.27140.2959235X-RAY DIFFRACTION47.25
3.56-3.630.33150.2576282X-RAY DIFFRACTION56.57
3.63-3.690.3092230.2653363X-RAY DIFFRACTION73.24
3.69-3.770.2101230.2787455X-RAY DIFFRACTION89.01
3.77-3.850.3238330.2834470X-RAY DIFFRACTION98.05
3.85-3.940.2454270.2661519X-RAY DIFFRACTION99.82
3.94-4.040.2599250.2413488X-RAY DIFFRACTION100
4.04-4.150.1994350.2355502X-RAY DIFFRACTION100
4.15-4.270.2888210.2464519X-RAY DIFFRACTION100
4.27-4.410.2846210.2245515X-RAY DIFFRACTION100
4.41-4.560.2405250.2394505X-RAY DIFFRACTION100
4.56-4.750.2453340.2197496X-RAY DIFFRACTION99.62
4.75-4.960.284320.2451505X-RAY DIFFRACTION100
4.96-5.220.3936280.2586523X-RAY DIFFRACTION99.82
5.22-5.540.3386240.2685509X-RAY DIFFRACTION100
5.55-5.970.3318210.2903526X-RAY DIFFRACTION100
5.97-6.560.3266320.3291515X-RAY DIFFRACTION100
6.57-7.50.2455270.2955537X-RAY DIFFRACTION100
7.5-9.380.2235310.1959530X-RAY DIFFRACTION100
9.4-28.360.2822330.2436532X-RAY DIFFRACTION93.08
Refinement TLS params.Method: refined / Origin x: 11.7463586445 Å / Origin y: -16.0976483841 Å / Origin z: 25.2379800437 Å
111213212223313233
T0.726597481425 Å20.141836721544 Å2-0.00673671339104 Å2-0.599358880219 Å20.206732238878 Å2--0.215209491871 Å2
L1.63964178101 °2-0.0640844119356 °20.598813260967 °2-0.968724305796 °2-0.189210295208 °2--1.70929353824 °2
S-0.128499877462 Å °-0.259151334857 Å °-0.453927337767 Å °0.538781099183 Å °-0.164631499274 Å °-0.284505625372 Å °0.715861351696 Å °0.423434651283 Å °-0.207669251254 Å °
Refinement TLS groupSelection details: all

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