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- EMDB-7009: Structure of an acid sensing ion channel in a resting state at high pH -

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Basic information

Entry
Database: EMDB / ID: 7009
TitleStructure of an acid sensing ion channel in a resting state at high pH
Map data
SampleAcid Sensing Ion Channel 1a
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
SourceGallus / bird / image: Gallus gallus
Methodsingle particle reconstruction, at 3.7 Å resolution
AuthorsYoder N / Yoshioka C
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 ReportPDB-ID: 6ave

SummaryFull reportAbout validation report
DateDeposition: Sep 2, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Mar 21, 2018 / Last update: Mar 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.93
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.93
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6ave
  • Surface level: 3.93
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_7009.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.04 Å/pix.
= 208. Å
200 pix
1.04 Å/pix.
= 208. Å
200 pix
1.04 Å/pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:3.93 (by author), 3.93 (movie #1):
Minimum - Maximum-30.670943999999999 - 50.753925000000002
Average (Standard dev.)0.030705905 (1.101586)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000208.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-30.67150.7540.031

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Supplemental data

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Sample components

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Entire Acid Sensing Ion Channel 1a

EntireName: Acid Sensing Ion Channel 1a / Number of components: 3
MassTheoretical: 180.03144 kDa

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Component #1: protein, Acid Sensing Ion Channel 1a

ProteinName: Acid Sensing Ion Channel 1a / Recombinant expression: No
MassTheoretical: 180.03144 kDa
SourceSpecies: Gallus / bird / image: Gallus gallus
Source (engineered)Expression System: Homo sapiens / human /

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Component #2: protein, Acid-sensing ion channel 1

ProteinName: Acid-sensing ion channel 1 / Recombinant expression: No
MassTheoretical: 60.080324 kDa
Source (engineered)Expression System: Gallus gallus / bird / Chicken /

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 3.2 mg/ml / pH: 8
Support film15 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 291.15 K / Humidity: 1 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 26117
3D reconstructionSoftware: FREALIGN / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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