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- PDB-6ave: Structure of an acid sensing ion channel in a resting state at high pH -

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Basic information

Entry
Database: PDB / ID: 6ave
TitleStructure of an acid sensing ion channel in a resting state at high pH
ComponentsAcid-sensing ion channel 1
KeywordsTRANSPORT PROTEIN / Ion channel / ASIC / ASIC1a / Sodium channel / MEMBRANE PROTEIN
Function / homologyStimuli-sensing channels / Amiloride-sensitive sodium channels signature. / Amiloride-sensitive sodium channel / Epithelial sodium channel, conserved site / Epithelial sodium channel, chordates / Epithelial sodium channel / acid-sensing ion channel activity / sensory perception of sour taste / cellular response to pH / sodium ion transmembrane transport ...Stimuli-sensing channels / Amiloride-sensitive sodium channels signature. / Amiloride-sensitive sodium channel / Epithelial sodium channel, conserved site / Epithelial sodium channel, chordates / Epithelial sodium channel / acid-sensing ion channel activity / sensory perception of sour taste / cellular response to pH / sodium ion transmembrane transport / negative regulation of neurotransmitter secretion / response to acidic pH / associative learning / behavioral fear response / response to amphetamine / regulation of membrane potential / calcium ion transmembrane transport / protein homotrimerization / memory / synapse / integral component of plasma membrane / Golgi apparatus / identical protein binding / Acid-sensing ion channel 1
Function and homology information
Specimen sourceGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsYoder, N. / Yoshioka, C. / Gouaux, E.
CitationJournal: Nature / Year: 2018
Title: Gating mechanisms of acid-sensing ion channels.
Authors: Nate Yoder / Craig Yoshioka / Eric Gouaux
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 2, 2017 / Release: Mar 21, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 21, 2018Structure modelrepositoryInitial release
1.1Mar 28, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Acid-sensing ion channel 1
B: Acid-sensing ion channel 1
C: Acid-sensing ion channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,5689
Polyers180,2413
Non-polymers1,3276
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)14410
ΔGint (kcal/M)-70
Surface area (Å2)56710

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Components

#1: Protein/peptide Acid-sensing ion channel 1 / / ASIC1 / Amiloride-sensitive cation channel 2 / neuronal


Mass: 60080.324 Da / Num. of mol.: 3 / Source: (gene. exp.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Production host: Homo sapiens (human) / References: UniProt: Q1XA76
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 6 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Acid Sensing Ion Channel 1a / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.18003144 MDa / Experimental value: NO
Source (natural)Organism: Gallus (bird)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer ID
1150 mMSodium Chloride1
220 mMTris Buffer pH 8.01
35 mMCalcium Chloride1
41 mMn-Dodecyl-b-D-Maltopyranoside1
50.2 mMCholesterol Hemisuccinate1
61 mMDithiothreitol1
SpecimenConc.: 3.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291.15 kelvins

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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 FIELDBright-field microscopy
Image recordingAverage exposure time: 10 sec. / Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1
Image scansMovie frames/image: 100

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Processing

SoftwareName: PHENIX / Version: dev_2597: / Classification: refinement
EM software
IDNameVersionCategory
1DoG Pickerparticle selection
2SerialEM3.6.ximage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION2.1b1initial Euler assignment
11FREALIGNcisTEMfinal Euler assignment
12RELION2.1b1classification
13FREALIGNcisTEM3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C3
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 26117 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089915
ELECTRON MICROSCOPYf_angle_d0.94613518
ELECTRON MICROSCOPYf_dihedral_angle_d9.2765832
ELECTRON MICROSCOPYf_chiral_restr0.0681512
ELECTRON MICROSCOPYf_plane_restr0.0051755

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