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- PDB-5ipq: Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV... -

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Basic information

Entry
Database: PDB / ID: 5ipq
TitleCryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 2
Components
  • Ionotropic glutamate receptor subunit NR2B
  • N-methyl-D-aspartate receptor subunit NR1-8a
KeywordsSIGNALING PROTEIN / ligand-gated ion channel / synaptic transmission
Function / homology
Function and homology information


NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / response to zinc ion / response to magnesium ion / glutamate-gated calcium ion channel activity / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / excitatory postsynaptic potential ...NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / response to zinc ion / response to magnesium ion / glutamate-gated calcium ion channel activity / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / regulation of synaptic plasticity / calcium ion transmembrane transport / long-term synaptic potentiation / late endosome / signaling receptor activity / chemical synaptic transmission / postsynaptic membrane / lysosome / neuron projection / synapse / metal ion binding / plasma membrane
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.5 Å
AuthorsZhu, S. / Stein, A.R. / Yoshioka, C. / Lee, C.H. / Goehring, A. / Mchaourab, S.H. / Gouaux, E.
CitationJournal: Cell / Year: 2016
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
DepositionMar 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Experimental preparation
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_single_particle_entity / em_tomography_specimen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_single_particle_entity.point_symmetry / _em_tomography_specimen.id

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Assembly

Deposited unit
A: N-methyl-D-aspartate receptor subunit NR1-8a
B: Ionotropic glutamate receptor subunit NR2B
C: N-methyl-D-aspartate receptor subunit NR1-8a
D: Ionotropic glutamate receptor subunit NR2B


Theoretical massNumber of molelcules
Total (without water)371,7724
Polymers371,7724
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein N-methyl-D-aspartate receptor subunit NR1-8a


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.) Xenopus laevis (African clawed frog) / Production host: Homo sapiens (human) / References: UniProt: C0KD18, UniProt: A0A1L8F5J9*PLUS
#2: Protein Ionotropic glutamate receptor subunit NR2B


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.) Xenopus laevis (African clawed frog) / Gene: NR2B / Production host: Homo sapiens (human) / References: UniProt: A7XY94

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GluN1-GluN2B receptor in the complex with competitive antagonists DCKA and D-APV
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Homo sapiens (human) / Cell: GnTI- / Plasmid: pEGBacmam
Buffer solutionpH: 6.5
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 18 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 0.01 mm
Image recordingElectron dose: 10.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION1.3particle selection
2SerialEMimage acquisition
4RELION1.3CTF correction
12RELION1.3classification
13RELION1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 393513
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38007 / Symmetry type: POINT

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