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

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Basic information

Entry
Database: PDB / ID: 24jt
TitleCrystal structure of voltage-gated sodium channel NavAb N49K 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 RM4018 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 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
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

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7464
Polymers26,5641
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)110,98616
Polymers106,2564
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 area11660 Å2
ΔGint-131 kcal/mol
Surface area49030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.280, 128.280, 202.360
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: 26563.896 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: 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
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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: 7.83 Å3/Da / Density % sol: 84.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 7%-9% PEG 6000, 100mM sodium chloride, 100mM magnesium nitrate, 100mM cadmium nitrate, 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 EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→45.35 Å / Num. obs: 6934 / % possible obs: 89.27 % / Redundancy: 103.9 % / Biso Wilson estimate: 178.88 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.0965 / Net I/σ(I): 11.31
Reflection shellResolution: 4.1→4.247 Å / Num. unique obs: 263 / CC1/2: 0.448 / Rpim(I) all: 0.5743

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→45.35 Å / SU ML: 0.7493 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.9815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3747 290 4.67 %
Rwork0.354 5926 -
obs0.3547 6216 89.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 194.81 Å2
Refinement stepCycle: LAST / Resolution: 4.1→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 68 0 1779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531830
X-RAY DIFFRACTIONf_angle_d0.89992491
X-RAY DIFFRACTIONf_chiral_restr0.0571309
X-RAY DIFFRACTIONf_plane_restr0.0057280
X-RAY DIFFRACTIONf_dihedral_angle_d15.4648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.170.599330.4566115X-RAY DIFFRACTION35.22
4.17-4.250.454350.4063141X-RAY DIFFRACTION42.82
4.25-4.330.525110.3684163X-RAY DIFFRACTION53.21
4.33-4.420.3892150.411237X-RAY DIFFRACTION73.68
4.42-4.510.4414190.3862284X-RAY DIFFRACTION88.34
4.51-4.620.4631190.3754301X-RAY DIFFRACTION94.96
4.62-4.730.4698110.3388329X-RAY DIFFRACTION100
4.73-4.860.3888210.3501318X-RAY DIFFRACTION100
4.86-50.5109110.378331X-RAY DIFFRACTION100
5-5.160.2853130.3761328X-RAY DIFFRACTION99.71
5.16-5.350.3632140.3564327X-RAY DIFFRACTION99.42
5.35-5.560.4403180.3938314X-RAY DIFFRACTION99.7
5.56-5.820.2764180.3272335X-RAY DIFFRACTION100
5.82-6.120.4175180.3651331X-RAY DIFFRACTION100
6.12-6.50.4471100.4421337X-RAY DIFFRACTION99.71
6.51-70.3219210.4023327X-RAY DIFFRACTION100
7.01-7.70.2561140.3242333X-RAY DIFFRACTION100
7.71-8.810.3515210.2944341X-RAY DIFFRACTION100
8.82-11.070.2822140.2443351X-RAY DIFFRACTION99.73
11.1-45.350.417140.3955383X-RAY DIFFRACTION98.27

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