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Yorodumi- EMDB-21381: Structure of an acid-sensing ion channel solubilized by styrene m... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21381 | ||||||||||||
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Title | Structure of an acid-sensing ion channel solubilized by styrene maleic acid and in a resting state at high pH | ||||||||||||
Map data | Map of an acid-sensing ion channel solubilized by styrene maleic acid and in a resting state at high pH. | ||||||||||||
Sample |
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Function / homology | Function and homology information pH-gated monoatomic ion channel activity / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / protein homotrimerization / sodium ion transmembrane transport / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Gallus gallus (chicken) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.65 Å | ||||||||||||
Authors | Yoder N / Gouaux E | ||||||||||||
Funding support | United States, 3 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21381.map.gz | 244.4 MB | EMDB map data format | |
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Header (meta data) | emd-21381-v30.xml emd-21381.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_21381.png | 47.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21381 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21381 | HTTPS FTP |
-Validation report
Summary document | emd_21381_validation.pdf.gz | 416.1 KB | Display | EMDB validaton report |
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Full document | emd_21381_full_validation.pdf.gz | 415.6 KB | Display | |
Data in XML | emd_21381_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_21381_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21381 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21381 | HTTPS FTP |
-Related structure data
Related structure data | 6vtlMC 6vtkC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21381.map.gz / Format: CCP4 / Size: 259.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of an acid-sensing ion channel solubilized by styrene maleic acid and in a resting state at high pH. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.648 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Acid-sensing ion channel
Entire | Name: Acid-sensing ion channel |
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Components |
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-Supramolecule #1: Acid-sensing ion channel
Supramolecule | Name: Acid-sensing ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Gallus gallus (chicken) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: Acid-sensing ion channel 1
Macromolecule | Name: Acid-sensing ion channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 60.080324 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.00 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen 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.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 48338 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2) |