[English] 日本語
![](img/lk-miru.gif)
- EMDB-44125: Structure of concanavalin A (ConA) dimer from the open-state stru... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||||||||||
![]() | ||||||||||||||||
![]() |
| |||||||||||||||
![]() | kainate receptor / GluK2 / glutamate / positive allosteric modulator / BPAM344 / open / concanavalin A / ConA / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.58 Å | |||||||||||||||
![]() | Nadezhdin KD / Gangwar SP / Sobolevsky AI | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 51.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 74.5 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 50.5 MB 50.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 781.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 780.7 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9b34MC ![]() 9b33C ![]() 9b35C ![]() 9b36C ![]() 9b37C ![]() 9b38C ![]() 9b39C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.3487 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_44125_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_44125_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Concanavalin-A dimer
Entire | Name: Concanavalin-A dimer |
---|---|
Components |
|
-Supramolecule #1: Concanavalin-A dimer
Supramolecule | Name: Concanavalin-A dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50 KDa |
-Macromolecule #1: Concanavalin A
Macromolecule | Name: Concanavalin A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.622385 KDa |
Sequence | String: ADTIVAVELD TYPNTDIGDP SYPHIGIDIK SVRSKKTAKW NMQNGKVGTA HIIYNSVDKR LSAVVSYPNA DSATVSYDVD LDNVLPEWV RVGLSASTGL YKETNTILSW SFTSKLKSNS THETNALHFM FNQFSKDQKD LILQGDATTG TDGNLELTRV S SNGSPQGS ...String: ADTIVAVELD TYPNTDIGDP SYPHIGIDIK SVRSKKTAKW NMQNGKVGTA HIIYNSVDKR LSAVVSYPNA DSATVSYDVD LDNVLPEWV RVGLSASTGL YKETNTILSW SFTSKLKSNS THETNALHFM FNQFSKDQKD LILQGDATTG TDGNLELTRV S SNGSPQGS SVGRALFYAP VHIWESSAVV ASFEATFTFL IKSPDSHPAD GIAFFISNID SSIPSGSTGR LLGLFPDAN UniProtKB: Concanavalin-A, Concanavalin-A |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA |
---|---|
Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 Component:
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 5 / Number real images: 22990 / Average exposure time: 2.5 sec. / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | ![]() PDB-9b34: |