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- PDB-6ksp: Rat GluD1 receptor(splayed conformation) in complex with 7-CKA an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ksp | ||||||
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Title | Rat GluD1 receptor(splayed conformation) in complex with 7-CKA and Calcium ions | ||||||
![]() | Glutamate receptor ionotropic, delta-1 | ||||||
![]() | MEMBRANE PROTEIN / complex | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.1 Å | ||||||
![]() | Burada, A.P. / 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 | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 505.5 KB | Display | ![]() |
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PDB format | ![]() | 412.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0773MC ![]() 0774C ![]() 6kssC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 95718.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Compound details | The distance between Residue A LYS 527 and Residue A ILE 532 is 20.50 Angstrom. The distance ...The distance between Residue A LYS 527 and Residue A ILE 532 is 20.50 Angstrom. The distance between Residue B LYS 527 and Residue B ILE 532 is 22.35 Angstrom. The distance between Residue C LYS 527 and Residue C ILE 532 is 20.85 Angstrom. | Sequence details | Thrombin recognition site | |
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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 |
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Sample preparation
Component | Name: GluD1 / Type: COMPLEX / Details: Recombinantly expressed protein / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.388 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 / Details: 20mM Tris, 150mM NaCl, 0.75mM DDM, 0.025mM CHS |
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 6 sec. / Electron dose: 40.38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4120 |
Image scans | Movie frames/image: 40 / Used frames/image: 0-40 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2000 Details: Particles were picked manually, which were used as reference for autopicking. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14939 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |