[English] 日本語
Yorodumi
- PDB-9vdu: Crystal structure of voltage-gated sodium channel NavAb N49K/L176... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vdu
TitleCrystal structure of voltage-gated sodium channel NavAb N49K/L176F 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: 3.4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,33111
Polymers26,9001
Non-polymers5,43010
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)129,32344
Polymers107,6014
Non-polymers21,72240
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 area27990 Å2
ΔGint-163 kcal/mol
Surface area49220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.520, 128.520, 200.790
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-1401-

HOH

31A-1403-

HOH

41A-1404-

HOH

-
Components

#1: Protein Ion transport protein


Mass: 26900.197 Da / Num. of mol.: 1 / Mutation: N49K/L176F
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.: 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
#4: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 7.71 Å3/Da / Density % sol: 84.04 %
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

-
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: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→29.68 Å / Num. obs: 11918 / % possible obs: 99.15 % / Redundancy: 104.7 % / Biso Wilson estimate: 88.46 Å2 / CC1/2: 0.985 / Rpim(I) all: 0.03249 / Net I/σ(I): 24.75
Reflection shellResolution: 3.4→3.5 Å / Mean I/σ(I) obs: 3.44 / Num. unique obs: 1085 / CC1/2: 0.932 / Rpim(I) all: 0.3729

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→29.68 Å / SU ML: 0.4281 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.7095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3039 574 4.84 %
Rwork0.2538 11276 -
obs0.256 11850 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.12 Å2
Refinement stepCycle: LAST / Resolution: 3.4→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 355 5 2155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01012193
X-RAY DIFFRACTIONf_angle_d1.44622929
X-RAY DIFFRACTIONf_chiral_restr0.0761328
X-RAY DIFFRACTIONf_plane_restr0.0072308
X-RAY DIFFRACTIONf_dihedral_angle_d22.297920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.460.3003240.2576516X-RAY DIFFRACTION92.47
3.46-3.520.2506210.2321524X-RAY DIFFRACTION96.46
3.52-3.590.2741240.219572X-RAY DIFFRACTION100
3.59-3.660.2239260.2048565X-RAY DIFFRACTION100
3.66-3.740.2278310.1968535X-RAY DIFFRACTION100
3.74-3.830.2441240.2216561X-RAY DIFFRACTION100
3.83-3.920.3625170.2176570X-RAY DIFFRACTION99.83
3.92-4.030.2689410.2142553X-RAY DIFFRACTION99.83
4.03-4.150.2843200.2037562X-RAY DIFFRACTION100
4.15-4.280.3652340.2232564X-RAY DIFFRACTION100
4.28-4.430.292380.2482551X-RAY DIFFRACTION100
4.43-4.610.2917230.2429569X-RAY DIFFRACTION100
4.61-4.820.2577320.2084552X-RAY DIFFRACTION99.83
4.82-5.070.3589340.2364555X-RAY DIFFRACTION100
5.07-5.390.2725250.251586X-RAY DIFFRACTION100
5.39-5.80.2876270.3113570X-RAY DIFFRACTION100
5.8-6.380.3686350.3498569X-RAY DIFFRACTION100
6.38-7.290.3412270.3002584X-RAY DIFFRACTION100
7.29-9.140.2781340.2478593X-RAY DIFFRACTION100
9.15-29.680.3426370.2999625X-RAY DIFFRACTION99.4
Refinement TLS params.Method: refined / Origin x: 12.2644305879 Å / Origin y: -16.4997669234 Å / Origin z: 25.4396643914 Å
111213212223313233
T0.86515310836 Å20.111763578175 Å2-0.03779411405 Å2-0.644867495324 Å20.180257499855 Å2--0.482140179708 Å2
L3.30588615339 °2-0.805913759156 °20.935045013224 °2-1.43112219331 °2-0.0797470226469 °2--2.57895853804 °2
S-0.078353136822 Å °-0.444008912617 Å °-0.230811353738 Å °0.548170713083 Å °0.00650193988653 Å °-0.265710966555 Å °0.700846514709 Å °0.386306497142 Å °0.0340590867559 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more