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- PDB-5iou: Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5iou | ||||||
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Title | Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine-bound conformation | ||||||
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![]() | SIGNALING PROTEIN / ligand-gated ion channel / synaptic transmission | ||||||
Function / homology | ![]() NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to zinc ion / response to magnesium ion / regulation of membrane potential / excitatory postsynaptic potential / long-term synaptic potentiation / late endosome / chemical synaptic transmission / postsynaptic membrane ...NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to zinc ion / response to magnesium ion / regulation of membrane potential / excitatory postsynaptic potential / long-term synaptic potentiation / late endosome / chemical synaptic transmission / postsynaptic membrane / lysosome / neuron projection / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | ||||||
![]() | Zhu, S. / Stein, A.R. / Yoshioka, C. / Lee, C.H. / Goehring, A. / Mchaourab, S.H. / Gouaux, E. | ||||||
![]() | ![]() Title: Mechanism of NMDA Receptor Inhibition and Activation. Authors: Shujia Zhu / Richard A Stein / Craig Yoshioka / Chia-Hsueh Lee / April Goehring / Hassane S Mchaourab / Eric Gouaux / ![]() Abstract: N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated, calcium-permeable ion channels that mediate synaptic transmission and underpin learning and memory. NMDAR dysfunction is directly ...N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated, calcium-permeable ion channels that mediate synaptic transmission and underpin learning and memory. NMDAR dysfunction is directly implicated in diseases ranging from seizure to ischemia. Despite its fundamental importance, little is known about how the NMDAR transitions between inactive and active states and how small molecules inhibit or activate ion channel gating. Here, we report electron cryo-microscopy structures of the GluN1-GluN2B NMDA receptor in an ensemble of competitive antagonist-bound states, an agonist-bound form, and a state bound with agonists and the allosteric inhibitor Ro25-6981. Together with double electron-electron resonance experiments, we show how competitive antagonists rupture the ligand binding domain (LBD) gating "ring," how agonists retain the ring in a dimer-of-dimers configuration, and how allosteric inhibitors, acting within the amino terminal domain, further stabilize the LBD layer. These studies illuminate how the LBD gating ring is fundamental to signal transduction and gating in NMDARs. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 440.2 KB | Display | ![]() |
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PDB format | ![]() | 288.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 922.7 KB | Display | ![]() |
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Full document | ![]() | 938.5 KB | Display | |
Data in XML | ![]() | 67.7 KB | Display | |
Data in CIF | ![]() | 109.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8097MC ![]() 8098C ![]() 8101C ![]() 8102C ![]() 8103C ![]() 8104C ![]() 8105C ![]() 8106C ![]() 5iovC ![]() 5ipqC ![]() 5iprC ![]() 5ipsC ![]() 5iptC ![]() 5ipuC ![]() 5ipvC 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: 92651.234 Da / Num. of mol.: 2 Mutation: K51F, R52F, N300Q, N350Q, N368D, N440D, N469D, K493A, K494A, E495A, G610R, I617L, D656R, N769E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 93234.742 Da / Num. of mol.: 2 Mutation: M20S, G21R, C22A, A64E, N69Q, N343D, T490V, V615L, E654R, E655R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | #4: Chemical | |
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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: GluN1-GluN2B NMDA receptor / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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 / Nominal defocus max: 4000 nm / Nominal defocus min: 2500 nm / Cs: 2 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 8 sec. / Electron dose: 8.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
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Processing
EM software | Name: RELION / Version: 1.3 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 185009 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116968 / Symmetry type: POINT |
Refinement | Highest resolution: 7 Å |