[English] 日本語
Yorodumi- EMDB-7009: Structure of an acid sensing ion channel in a resting state at high pH -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7009 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of an acid sensing ion channel in a resting state at high pH | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
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 (bird) / Gallus gallus (chicken) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Yoder N / Yoshioka C / Gouaux E | ||||||||||||
Funding support | United States, 3 items
| ||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7009.map.gz | 23.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-7009-v30.xml emd-7009.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
Images | emd_7009.png | 148.5 KB | ||
Others | emd_7009_additional.map.gz emd_7009_half_map_1.map.gz emd_7009_half_map_2.map.gz | 28.3 MB 13.8 MB 13.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7009 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7009 | HTTPS FTP |
-Validation report
Summary document | emd_7009_validation.pdf.gz | 625.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_7009_full_validation.pdf.gz | 624.6 KB | Display | |
Data in XML | emd_7009_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | emd_7009_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7009 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7009 | HTTPS FTP |
-Related structure data
Related structure data | 6aveMC 5wkuC 5wkvC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_7009.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: #1
File | emd_7009_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_7009_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_7009_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Acid Sensing Ion Channel 1a
Entire | Name: Acid Sensing Ion Channel 1a |
---|---|
Components |
|
-Supramolecule #1: Acid Sensing Ion Channel 1a
Supramolecule | Name: Acid Sensing Ion Channel 1a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Gallus (bird) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 180.03144 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 |
---|---|
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 |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.2 mg/mL | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||||
Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Details: 15 mA | ||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film 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 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 |
---|---|
Final reconstruction | Number 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 assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1b1) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cisTEM |
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | PDB-6ave: |