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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: EMD-7009
TitleStructure of an acid sensing ion channel in a resting state at high pH
Map data
Sample
  • Complex: Acid Sensing Ion Channel 1a
    • Protein or peptide: Acid-sensing ion channel 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIon channel / ASIC / ASIC1a / Sodium channel / TRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


Stimuli-sensing channels / pH-gated monoatomic ion channel activity / cellular response to pH / ligand-gated sodium channel activity / sodium ion transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
Acid-sensing ion channel 1
Similarity search - Component
Biological speciesGallus (bird) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYoder N / Yoshioka C
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32DK007680 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)5R01NS038631 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)5F31NS096782 United States
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.
History
DepositionSep 2, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseMar 21, 2018-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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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
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  • 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

emd_7009.png

Downloads & links

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Map

FileDownload / File: emd_7009.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.93 / Movie #1: 3.93
Minimum - Maximum-30.670943999999999 - 50.753925000000002
Average (Standard dev.)0.030705905 (±1.101586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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-64-64-64
NX/NY/NZ128128128
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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Additional map: #1

Fileemd_7009_additional.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_7009_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_7009_half_map_2.map
Projections & Slices
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Sample components

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Entire : Acid Sensing Ion Channel 1a

EntireName: Acid Sensing Ion Channel 1a
Components
  • Complex: Acid Sensing Ion Channel 1a
    • Protein or peptide: Acid-sensing ion channel 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Acid Sensing Ion Channel 1a

SupramoleculeName: Acid Sensing Ion Channel 1a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus (bird)
Molecular weightTheoretical: 180.03144 KDa

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Macromolecule #1: Acid-sensing ion channel 1

MacromoleculeName: Acid-sensing ion channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 60.080324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMDLKVDEEE VDSGQPVSIQ AFASSSTLHG ISHIFSYERL SLKRVVWALC FMGSLALLAL VCTNRIQYYF LYPHVTKLDE VAATRLTFP AVTFCNLNEF RFSRVTKNDL YHAGELLALL NNRYEIPDTQ TADEKQLEIL QDKANFRNFK PKPFNMLEFY D RAGHDIRE ...String:
MMDLKVDEEE VDSGQPVSIQ AFASSSTLHG ISHIFSYERL SLKRVVWALC FMGSLALLAL VCTNRIQYYF LYPHVTKLDE VAATRLTFP AVTFCNLNEF RFSRVTKNDL YHAGELLALL NNRYEIPDTQ TADEKQLEIL QDKANFRNFK PKPFNMLEFY D RAGHDIRE MLLSCFFRGE QCSPEDFKVV FTRYGKCYTF NAGQDGKPRL ITMKGGTGNG LEIMLDIQQD EYLPVWGETD ET SFEAGIK VQIHSQDEPP LIDQLGFGVA PGFQTFVSCQ EQRLIYLPPP WGDCKATTGD SEFYDTYSIT ACRIDCETRY LVE NCNCRM VHMPGDAPYC TPEQYKECAD PALDFLVEKD NEYCVCEMPC NVTRYGKELS MVKIPSKASA KYLAKKYNKS EQYI GENIL VLDIFFEALN YETIEQKKAY EVAGLLGDIG GQMGLFIGAS ILTVLELFDY AYEVIKHRLC RRGKCRKNHK RNNTD KGVA LSMDDVKRHN PCESLRGHPA GMTYAANILP HHPARGTFED FTC

UniProtKB: Acid-sensing ion channel 1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.2 mg/mL
BufferpH: 8
Component:
ConcentrationName
150.0 mMSodium Chloride
20.0 mMTris Buffer pH 8.0
5.0 mMCalcium Chloride
1.0 mMn-Dodecyl-b-D-Maltopyranoside
0.2 mMCholesterol Hemisuccinate
1.0 mMDithiothreitol
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 26117
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1b1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM

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Atomic model buiding 1

RefinementSpace: REAL
Output model

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

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