[English] 日本語
- PDB-5x0m: Structure of a eukaryotic voltage-gated sodium channel at near at... -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 5x0m
TitleStructure of a eukaryotic voltage-gated sodium channel at near atomic resolution
DescriptorSodium channel protein
KeywordsMEMBRANE PROTEIN / ion channel / membrane protein
Specimen sourcePeriplaneta americana / arthropod / American cockroach / ワモンゴキブリ
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
AuthorsShen, H. / Zhou, Q. / Pan, X. / Li, Z. / Wu, J. / Yan, N.
CitationScience, 2017, 355

Science, 2017, 355 Yorodumi Papers
Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution.
Huaizong Shen / Qiang Zhou / Xiaojing Pan / Zhangqiang Li / Jianping Wu / Nieng Yan

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 21, 2017 / Release: Mar 8, 2017

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /

Downloads & links


Deposited unit
A: Sodium channel protein
hetero molecules

Theoretical massNumber of molelcules
Total (without water)188,01221

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3250
ΔGint (kcal/M)40
Surface area (Å2)71130


#1: Polypeptide(L)Sodium channel protein

Mass: 183875.422 Da / Num. of mol.: 1
Source: (gene. exp.) Periplaneta americana / arthropod / ワモンゴキブリ
References: UniProt: D0E0C2

Cellular component

Molecular function

#2: Chemical

Mass: 221.208 Da / Num. of mol.: 13 / Formula: C8H15NO6
#3: Chemical

Mass: 180.156 Da / Num. of mol.: 7 / Formula: C6H12O6

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: voltage-gated sodium channel / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Periplaneta americana
Source (recombinant)Organism: Homo sapiens
Buffer solutionDetails: 25 mM Tris-HCl, pH 7.4, 50mM NaCl, 0.1% digitonin, 2.5 mM D-Desthiobiotin and protease inhibitor cocktail
pH: 7.4
SpecimenConc.: 1 mg/ml / Details: This sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil Cu R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 kelvins
Details: Grids were blotted for 3.5 s and flash-frozen in liquid ethane cooled by liquid nitrogen.

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 / Calibrated defocus min: 1700 nm / Calibrated defocus max: 2600 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.5625 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32 / Used frames/image: 1-32


EM software
IDNameVersionCategoryImage processing IDImaging ID
Particle selectionNumber of particles selected: 4739175
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 1373581 / Symmetry type: POINT

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more