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Yorodumi- PDB-9b34: Structure of concanavalin A (ConA) dimer from the open-state stru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9b34 | |||||||||||||||
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Title | Structure of concanavalin A (ConA) dimer from the open-state structure of kainate receptor GluK2 in complex with agonist glutamate and positive allosteric modulator BPAM344 bound to two ConA dimers. Type I interface between GluK2 ligand-binding domain and ConA | |||||||||||||||
Components | Concanavalin A | |||||||||||||||
Keywords | MEMBRANE PROTEIN / kainate receptor / GluK2 / glutamate / positive allosteric modulator / BPAM344 / open / concanavalin A / ConA | |||||||||||||||
Function / homology | Function and homology information regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Canavalia ensiformis (jack bean) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å | |||||||||||||||
Authors | Nadezhdin, K.D. / Gangwar, S.P. / Sobolevsky, A.I. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nature / Year: 2024 Title: Kainate receptor channel opening and gating mechanism. Authors: Shanti Pal Gangwar / Maria V Yelshanskaya / Kirill D Nadezhdin / Laura Y Yen / Thomas P Newton / Muhammed Aktolun / Maria G Kurnikova / Alexander I Sobolevsky / Abstract: Kainate receptors, a subclass of ionotropic glutamate receptors, are tetrameric ligand-gated ion channels that mediate excitatory neurotransmission. Kainate receptors modulate neuronal circuits and ...Kainate receptors, a subclass of ionotropic glutamate receptors, are tetrameric ligand-gated ion channels that mediate excitatory neurotransmission. Kainate receptors modulate neuronal circuits and synaptic plasticity during the development and function of the central nervous system and are implicated in various neurological and psychiatric diseases, including epilepsy, depression, schizophrenia, anxiety and autism. Although structures of kainate receptor domains and subunit assemblies are available, the mechanism of kainate receptor gating remains poorly understood. Here we present cryo-electron microscopy structures of the kainate receptor GluK2 in the presence of the agonist glutamate and the positive allosteric modulators lectin concanavalin A and BPAM344. Concanavalin A and BPAM344 inhibit kainate receptor desensitization and prolong activation by acting as a spacer between the amino-terminal and ligand-binding domains and a stabilizer of the ligand-binding domain dimer interface, respectively. Channel opening involves the kinking of all four pore-forming M3 helices. Our structures reveal the molecular basis of kainate receptor gating, which could guide the development of drugs for treatment of neurological disorders. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9b34.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9b34.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 9b34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b34_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 9b34_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9b34_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 9b34_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/9b34 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/9b34 | HTTPS FTP |
-Related structure data
Related structure data | 44125MC 9b33C 9b35C 9b36C 9b37C 9b38C 9b39C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866 #2: Chemical | #3: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Concanavalin-A dimer / Type: COMPLEX / Entity ID: #1 / Source: NATURAL | ||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.05 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Canavalia ensiformis (jack bean) | ||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: Human embryonic kidney 293 / Plasmid: pEG BacMam | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 5 / Num. of real images: 22990 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8660229 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163519 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Space: REAL |