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

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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/homologyacid-sensing ion channel activity / Epithelial sodium channel, chordates / sensory perception of sour taste / Epithelial sodium channel, conserved site / Epithelial sodium channel / Amiloride-sensitive sodium channels signature. / Amiloride-sensitive sodium channel / Stimuli-sensing channels / negative regulation of neurotransmitter secretion / cellular response to pH ...acid-sensing ion channel activity / Epithelial sodium channel, chordates / sensory perception of sour taste / Epithelial sodium channel, conserved site / Epithelial sodium channel / Amiloride-sensitive sodium channels signature. / Amiloride-sensitive sodium channel / Stimuli-sensing channels / negative regulation of neurotransmitter secretion / cellular response to pH / sodium ion transmembrane transport / response to acidic pH / associative learning / calcium ion transmembrane transport / regulation of membrane potential / 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 / bird / Chicken /
MethodElectron microscopy (3.7 Å resolution / Particle / Single particle) / Transmission electron microscopy
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
Abstract: Acid-sensing ion channels (ASICs) are trimeric, proton-gated and sodium-selective members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed ...Acid-sensing ion channels (ASICs) are trimeric, proton-gated and sodium-selective members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout vertebrate central and peripheral nervous systems. Gating of ASICs occurs on a millisecond time scale and the mechanism involves three conformational states: high pH resting, low pH open and low pH desensitized. Existing X-ray structures of ASIC1a describe the conformations of the open and desensitized states, but the structure of the high pH resting state and detailed mechanisms of the activation and desensitization of the channel have remained elusive. Here we present structures of the high pH resting state of homotrimeric chicken (Gallus gallus) ASIC1a, determined by X-ray crystallography and single particle cryo-electron microscopy, and present a comprehensive molecular mechanism for proton-dependent gating in ASICs. In the resting state, the position of the thumb domain is further from the three-fold molecular axis, thereby expanding the 'acidic pocket' in comparison to the open and desensitized states. Activation therefore involves 'closure' of the thumb into the acidic pocket, expansion of the lower palm domain and an iris-like opening of the channel gate. Furthermore, we demonstrate how the β11-β12 linkers that demarcate the upper and lower palm domains serve as a molecular 'clutch', and undergo a simple rearrangement to permit rapid desensitization.
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 / bird / Chicken / / Gene: ASIC1, ACCN2 / Production host: Homo sapiens / 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

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Sample preparation

ComponentName: Acid Sensing Ion Channel 1a / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.18003144 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Gallus
Source (recombinant)Organism: Homo sapiens
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameBuffer ID
1150mMSodium Chloride1
220mMTris Buffer pH 8.01
35mMCalcium Chloride1
41mMn-Dodecyl-b-D-Maltopyranoside1
50.2mMCholesterol Hemisuccinate1
61mMDithiothreitol1
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 FIELD
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
13FREALIGNcisTEMRECONSTRUCTION
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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