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- PDB-5x0m: Structure of a eukaryotic voltage-gated sodium channel at near at... -

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Entry
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

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Assembly

Deposited unit
A: Sodium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,01221
Polyers183,8751
Non-polymers4,13720
Water0
#1


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

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Components

#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
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 13 / Formula: C8H15NO6
#3: Chemical
ChemComp-BMA / BETA-D-MANNOSE


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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.

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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

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging ID
1RELION1.4PARTICLE SELECTION1
2UCSF Image4IMAGE ACQUISITION1
4GctfCTF CORRECTION1
12RELION2.0CLASSIFICATION1
13RELION2.0RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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

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