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- EMDB-0774: Rat GluD1 receptor(compact conformation) in complex with 7-CKA an... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0774 | |||||||||
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Title | Rat GluD1 receptor(compact conformation) in complex with 7-CKA and Calcium ions | |||||||||
![]() | final refined map | |||||||||
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Function / homology | ![]() glutamate receptor activity / regulation of postsynapse organization / social behavior / GABA-ergic synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / postsynaptic membrane / glutamatergic synapse ...glutamate receptor activity / regulation of postsynapse organization / social behavior / GABA-ergic synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / postsynaptic membrane / glutamatergic synapse / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.1 Å | |||||||||
![]() | Burada AP / Kumar J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of the ionotropic glutamate receptor GluD1 reveal a non-swapped architecture. Authors: Ananth Prasad Burada / Rajesh Vinnakota / Janesh Kumar / ![]() Abstract: Ionotropic orphan delta (GluD) receptors are not gated by glutamate or any other endogenous ligand but are grouped with ionotropic glutamate receptors (iGluRs) based on sequence similarity. GluD1 ...Ionotropic orphan delta (GluD) receptors are not gated by glutamate or any other endogenous ligand but are grouped with ionotropic glutamate receptors (iGluRs) based on sequence similarity. GluD1 receptors play critical roles in synaptogenesis and synapse maintenance and have been implicated in neuronal disorders, including schizophrenia, cognitive deficits, and cerebral ataxia. Here we report cryo-EM structures of the rat GluD1 receptor complexed with calcium and the ligand 7-chlorokynurenic acid (7-CKA), elucidating molecular architecture and principles of receptor assembly. The structures reveal a non-swapped architecture at the interface of the extracellular amino-terminal domain (ATD) and the ligand-binding domain (LBD). This finding is in contrast with structures of other families of iGluRs, where the dimer partners between the ATD and LBD layers are swapped. Our results demonstrate that principles of architecture and symmetry are not conserved between delta receptors and other iGluRs and provide a molecular blueprint for understanding the functions of the 'orphan' class of iGluRs. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 226.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
Images | ![]() | 41.1 KB | ||
Others | ![]() ![]() | 226.8 MB 226.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kssMC ![]() 0773C ![]() 6kspC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 6.5 TB Data #1: ionotropioc Glutamate receptor Delta1 [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | final refined map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map A
File | emd_0774_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_0774_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : GluD1
Entire | Name: GluD1 |
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Components |
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-Supramolecule #1: GluD1
Supramolecule | Name: GluD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Recombinantly expressed protein |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Experimental: 388 KDa |
-Macromolecule #1: Glutamate receptor ionotropic, delta-1
Macromolecule | Name: Glutamate receptor ionotropic, delta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 95.718039 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DSIIHIGAIF EENAAKDDRV FQLAVSDLSL NDDILQSEKI TYSIKVIEAN NPFQAVQEAC DLMTQGILAL VTSTGCASAN ALQSLTDAM HIPHLFVQRN PGGSPRTACH LNPSPDGEAY TLASRPPVRL NDVMLRLVTE LRWQKFVMFY DSEYDIRGLQ S FLDQASRL ...String: DSIIHIGAIF EENAAKDDRV FQLAVSDLSL NDDILQSEKI TYSIKVIEAN NPFQAVQEAC DLMTQGILAL VTSTGCASAN ALQSLTDAM HIPHLFVQRN PGGSPRTACH LNPSPDGEAY TLASRPPVRL NDVMLRLVTE LRWQKFVMFY DSEYDIRGLQ S FLDQASRL GLDVSLQKVD KNISHVFTSL FTTMKTEELN RYRDTLRRAI LLLSPQGAHS FINEAVETNL ASKDSHWVFV NE EISDPEI LDLVHSALGR MTVVRQIFPS AKDNQKCMRN NHRISSLLCD PQEGYLQMLQ ISNLYLYDSV LMLANAFHRK LED RKWHSM ASLNCIRKST KPWNGGRSML DTIKKGHITG LTGVMEFRED SSNPYVQFEI LGTTYSETFG KDMRKLATWD SEKG LNGSL QERPMGSRLQ GLTLKVVTVL EEPFVMVAEN ILGQPKRYKG FSIDVLDALA KALGFKYEIY QAPDGRYGHQ LHNTS WNGM IGELISKRAD LAISAITITP ERESVVDFSK RYMDYSVGIL IKKPEEKISI FSLFAPFDFA VWACIAAAIP VVGVLI FVL NRIQAVRSQS ATQPRPSASA TLHSAIWIVY GAFVQQGGES SVNSVAMRIV MGSWWLFTLI VCSSYTANLA AFLTVSR MD SPVRTFQDLS KQLEMSYGTV RDSAVYEYFR AKGTNPLEQD STFAELWRTI SKNGGADNCV SNPSEGIRKA KKGNYAFL W DVAVVEYAAL TDDDCSVTVI GNSISSKGYG IALQHGSPYR DLFSQRILEL QDTGDLDVLK QKWWPHTGRC DLTSHSSAQ TDGKSLKLHS FAGVFCILAI GLLLACLVAA LELWWNSNRC HQETPKEDKE VGLVPR |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-6kss: |