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Yorodumi- EMDB-0979: Rat ionotropic Glutamate Delta-2 receptor in complex with 7-CKA a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0979 | |||||||||
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Title | Rat ionotropic Glutamate Delta-2 receptor in complex with 7-CKA and Calcium | |||||||||
Map data | refined map | |||||||||
Sample |
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Function / homology | Function and homology information excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly ...excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly / ionotropic glutamate receptor complex / prepulse inhibition / regulation of neuron apoptotic process / somatodendritic compartment / excitatory postsynaptic potential / synaptic transmission, glutamatergic / PDZ domain binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / protein localization / scaffold protein binding / postsynaptic membrane / dendritic spine / glutamatergic synapse / synapse / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.8 Å | |||||||||
Authors | Kumar J / Burada AP | |||||||||
Funding support | India, 1 items
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Citation | Journal: J Struct Biol / Year: 2020 Title: The architecture of GluD2 ionotropic delta glutamate receptor elucidated by cryo-EM. Authors: Ananth Prasad Burada / Rajesh Vinnakota / Janesh Kumar / Abstract: GluD2 receptor belongs to the orphan delta family of glutamate receptor ion channels. These receptors play key roles in synaptogenesis and synaptic plasticity and are associated with multiple ...GluD2 receptor belongs to the orphan delta family of glutamate receptor ion channels. These receptors play key roles in synaptogenesis and synaptic plasticity and are associated with multiple neuronal disorders like schizophrenia, autism spectrum disorder, cerebellar ataxia, intellectual disability, paraplegia, retinal dystrophy, etc. Despite the importance of these receptors in CNS, insights into full-length GluD2 receptor structure is missing till-date. Here we report cryo-electron microscopy structure of the rat GluD2 receptor in the presence of calcium ions and the ligand 7-chlorokynurenic acid, elucidating its 3D architecture. The structure reveals a non-swapped architecture at the extracellular amino-terminal (ATD), and ligand-binding domain (LBD) interface similar to that observed in GluD1; however, the organization and arrangement of the ATD and LBD domains in GluD2 are unique. While our results demonstrate that non-swapped architecture is conserved in the delta receptor family, they also highlight the differences that exist between the two member receptors; GluD1 and GluD2. | |||||||||
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_0979.map.gz | 42.8 MB | EMDB map data format | |
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Header (meta data) | emd-0979-v30.xml emd-0979.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_0979.png | 70 KB | ||
Masks | emd_0979_msk_1.map | 83.7 MB | Mask map | |
Others | emd_0979_half_map_1.map.gz emd_0979_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0979 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0979 | HTTPS FTP |
-Related structure data
Related structure data | 6lu9MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0979.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | refined map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0979_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_0979_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_0979_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GluD2
Entire | Name: GluD2 |
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Components |
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-Supramolecule #1: GluD2
Supramolecule | Name: GluD2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Recombinantly expressed protein |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI- / Recombinant plasmid: pEG Bac Mam |
Molecular weight | Experimental: 388 KDa |
-Macromolecule #1: Glutamate receptor ionotropic, delta-2
Macromolecule | Name: Glutamate receptor ionotropic, delta-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 98.692242 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DSIIHIGAIF DESAKKDDEV FRTAVGDLNQ NEEILQTEKI TFSVTFVDGN NPFQAVQEAC ELMNQGILAL VSSIGCTSAG SLQSLADAM HIPHLFIQRS TAGTPRSGCG LTRSNRNDDY TLSVRPPVYL NEVILRVVTE YAWQKFIIFY DSEYDIRGIQ E FLDKVSQQ ...String: DSIIHIGAIF DESAKKDDEV FRTAVGDLNQ NEEILQTEKI TFSVTFVDGN NPFQAVQEAC ELMNQGILAL VSSIGCTSAG SLQSLADAM HIPHLFIQRS TAGTPRSGCG LTRSNRNDDY TLSVRPPVYL NEVILRVVTE YAWQKFIIFY DSEYDIRGIQ E FLDKVSQQ GMDVALQKVE NNINKMITTL FDTMRIEELN RYRDTLRRAI LVMNPATAKS FISEVVETNL VAFDCHWIII NE EINDVDV QELVRRSIGR LTIIRQTFPV PQNISQRCFR GNHRISSTLC DPKDPFAQNM EISNLYIYDT VLLLANAFHK KLQ DRKWHS MASLSCIRKN SKPWQGGRSM LETIKKGGVN GLTGDLEFGE NGGNPNVHFE ILGTNYGEEL GRGVRKLGCW NPVT GLNGS LTDKKLENNM RGVVLRVVTV LEEPFVMVSE NVLGKPKKYQ GFSIDVLDAL SNYLGFNYEI YVAPDHKYGS PQEDG TWNG LVGELVFKRA DIGISALTIT PDRENVVDFT TRYMDYSVGV LLRRAEKTVD MFACLAPFDL SLWACIAGTV LLVGLL VYL LNWLNPPRLQ MGSMTSTTLY NSMWFVYGSF VQQGGEVPYT TLATRMMMGA WWLFALIVIS SYTANLAAFL TITRIES SI QSLQDLSKQT DIPYGTVLDS AVYQHVRMKG LNPFERDSMY SQMWRMINRS NGSENNVLES QAGIQKVKYG NYAFVWDA A VLEYVAINDP DCSFYTVGNT VADRGYGIAL QHGSPYRDVF SQRILELQQS GDMDILKHKW WPKNGQCDLY SSVDAKQKG GALDIKSLAG VFCILAAGIV LSCLIAVLET WWSRRKGSRV PSKEDDKEID LEHLHRRVNS LCTDDDSPHK GLVPRGS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 8 / Details: 20mM Tris, 150mM NaCl, 0.75mM DDM, 0.025mM CHS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 0-40 / Number real images: 4120 / Average exposure time: 6.0 sec. / Average electron dose: 40.38 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6lu9: |