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- PDB-5xsy: Structure of the Nav1.4-beta1 complex from electric eel -

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Entry
Database: PDB / ID: 5xsy
TitleStructure of the Nav1.4-beta1 complex from electric eel
DescriptorSodium channel protein
Voltage-gated sodium channel beta subunit 1
KeywordsMEMBRANE PROTEIN / voltage gated sodium channel
Specimen sourceElectrophorus electricus / fish / Electric eel / エレクトロフォルス・エレクトリクス, デンキウナギ
MethodElectron microscopy (4 Å resolution / Particle / Single particle)
AuthorsYan, Z. / Zhou, Q. / Wu, J.P. / Yan, N.
CitationCell, 2017, 170, 470-482.e11

Cell, 2017, 170, 470-482.e11 Yorodumi Papers
Structure of the Nav1.4-β1 Complex from Electric Eel.
Zhen Yan / Qiang Zhou / Lin Wang / Jianping Wu / Yanyu Zhao / Gaoxingyu Huang / Wei Peng / Huaizong Shen / Jianlin Lei / Nieng Yan

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 15, 2017 / Release: Aug 9, 2017

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Assembly

Deposited unit
A: Sodium channel protein
B: Voltage-gated sodium channel beta subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,47018
Polyers232,1772
Non-polymers3,29316
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6820
ΔGint (kcal/M)10
Surface area (Å2)71450

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Components

#1: Polypeptide(L)Sodium channel protein / Na(+) channel


Mass: 208519.797 Da / Num. of mol.: 1
Source: (natural) Electrophorus electricus / fish / エレクトロフォルス・エレクトリクス, デンキウナギ
References: UniProt: P02719

Cellular component

Molecular function

#2: Polypeptide(L)Voltage-gated sodium channel beta subunit 1


Mass: 23657.322 Da / Num. of mol.: 1
Source: (natural) Electrophorus electricus / fish / エレクトロフォルス・エレクトリクス, デンキウナギ
References: UniProt: A0A1L3MZ94

Cellular component

Molecular function

Biological process

#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 10 / Formula: C8H15NO6
#4: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 6 / 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 EeNav1.4 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1, 2 / Source: NATURAL
Source (natural)Organism: Electrophorus electricus
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2200 nm
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32

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Processing

SoftwareName: PHENIX / Version: dev_2405: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 123431 / Symmetry type: POINT
Refine
Refine IDHighest resolution
14.00
ELECTRON MICROSCOPY
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01210854
ELECTRON MICROSCOPYf_angle_d1.28714745
ELECTRON MICROSCOPYf_dihedral_angle_d12.8878617
ELECTRON MICROSCOPYf_chiral_restr0.0651748
ELECTRON MICROSCOPYf_plane_restr0.0081786

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