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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:
Acid-sensing ion channel 1 / ligand
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 / behavioral fear response / associative learning / regulation of membrane potential / response to amphetamine / 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
SourceGallus (bird)
Methodsingle particle reconstruction / cryo EM / 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
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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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.

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)
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 (chicken)

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

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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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