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- EMDB-21380: Structure of an acid-sensing ion channel solubilized by styrene m... -

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Basic information

Entry
Database: EMDB / ID: EMD-21380
TitleStructure of an acid-sensing ion channel solubilized by styrene maleic acid and in a desensitized state at low pH
Map dataMap of SMA-cASIC1a in a desensitized state at low pH.
Sample
  • Complex: Acid-sensing ion channel
    • Protein or peptide: Acid-sensing ion channel 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsion channel / ligand-gated ion channel / acid-sensing ion channel / ASIC / ASIC1a / proton-gated ion channel / membrane protein / TRANSPORT 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 / postsynaptic membrane / dendrite / 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 gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsYoder N / Gouaux E
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)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
Citation
Journal: Elife / Year: 2020
Title: The His-Gly motif of acid-sensing ion channels resides in a reentrant 'loop' implicated in gating and ion selectivity.
Authors: Nate Yoder / Eric Gouaux /
Abstract: Acid-sensing ion channels (ASICs) are proton-gated members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout the central and peripheral ...Acid-sensing ion channels (ASICs) are proton-gated members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout the central and peripheral nervous systems. The homotrimeric splice variant ASIC1a has been implicated in nociception, fear memory, mood disorders and ischemia. Here, we extract full-length chicken ASIC1 (cASIC1) from cell membranes using styrene maleic acid (SMA) copolymer, elucidating structures of ASIC1 channels in both high pH resting and low pH desensitized conformations by single-particle cryo-electron microscopy (cryo-EM). The structures of resting and desensitized channels reveal a reentrant loop at the amino terminus of ASIC1 that includes the highly conserved 'His-Gly' (HG) motif. The reentrant loop lines the lower ion permeation pathway and buttresses the 'Gly-Ala-Ser' (GAS) constriction, thus providing a structural explanation for the role of the His-Gly dipeptide in the structure and function of ASICs.
#1: Journal: Biorxiv / Year: 2020
Title: Conserved His-Gly motif of acid-sensing ion channels resides in a reentrant loop implicated in gating and ion selectivity
Authors: Yoder N / Gouaux E
History
DepositionFeb 12, 2020-
Header (metadata) releaseMar 11, 2020-
Map releaseMar 11, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.58
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.58
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vtk
  • Surface level: 0.58
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21380.png

Downloads & links

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Map

FileDownload / File: emd_21380.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of SMA-cASIC1a in a desensitized state at low pH.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 394.56 Å		1.1 Å/pix.
x 360 pix.
= 394.56 Å		1.1 Å/pix.
x 360 pix.
= 394.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.58 / Movie #1: 0.58
Minimum - Maximum-2.2550147 - 4.475725
Average (Standard dev.)-0.00047138782 (±0.066282846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z394.560394.560394.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-2.2554.476-0.000

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Supplemental data

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Sample components

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Entire : Acid-sensing ion channel

EntireName: Acid-sensing ion channel
Components
  • Complex: Acid-sensing ion channel
    • 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

SupramoleculeName: Acid-sensing ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 180 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

Concentration1.00 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER
Details: Specimen was frozen on a custom-made manual plunge apparatus in a cold room environment maintained at high humidity..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 121148
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)

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Atomic model buiding 1

Initial modelPDB ID:

4nyk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6vtk:
Structure of an acid-sensing ion channel solubilized by styrene maleic acid and in a desensitized state at low pH

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