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- PDB-5iou: Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/... -

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Entry
Database: PDB / ID: 5iou
TitleCryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine-bound conformation
Components
  • Ionotropic glutamate receptor subunit NR2B
  • N-methyl-D-aspartate receptor subunit NR1-8aNMDA receptor
KeywordsSIGNALING PROTEIN / ligand-gated ion channel / synaptic transmission
Function / homologyCalmodulin-binding domain C0, NMDA receptor, NR1 subunit / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Ligated ion channel L-glutamate- and glycine-binding site / N-methyl D-aspartate receptor 2B3 C-terminus / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Receptor family ligand binding region / Ligand-gated ion channel / Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ionotropic glutamate receptor ...Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Ligated ion channel L-glutamate- and glycine-binding site / N-methyl D-aspartate receptor 2B3 C-terminus / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Receptor family ligand binding region / Ligand-gated ion channel / Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ionotropic glutamate receptor / Ionotropic glutamate receptor, metazoa / Receptor, ligand binding region / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to magnesium ion / protein heterotetramerization / response to zinc ion / postsynaptic membrane / cell junction / integral component of plasma membrane / metal ion binding / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 1
Function and homology information
Specimen sourceXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 9, 2016 / Release: Apr 20, 2016
RevisionDateData content typeGroupProviderType
1.0Apr 20, 2016Structure modelrepositoryInitial release
1.1May 4, 2016Structure modelDatabase references

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)372,2168
Polyers371,7724
Non-polymers4444
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 92651.234 Da / Num. of mol.: 2
Mutation: K51F, R52F, N300Q, N350Q, N368D, N440D, N469D, K493A, K494A, E495A, G610R, I617L, D656R, N769E
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Homo sapiens (human) / References: UniProt: C0KD18, UniProt: A0A1L8F5J9*PLUS
#2: Protein/peptide 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: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: NR2B / Production host: Homo sapiens (human) / References: UniProt: A7XY94
#3: Chemical ChemComp-GLY / GLYCINE


Mass: 75.067 Da / Num. of mol.: 2 / Formula: C2H5NO2 / Glycine
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Mass: 147.129 Da / Num. of mol.: 2 / Formula: C5H9NO4 / Glutamic acid

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: GluN1-GluN2B NMDA receptor / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1,2 / Source: RECOMBINANT
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: unknown
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 2500 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 8.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM softwareName: RELION / Version: 1.3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 185009
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 116968 / Symmetry type: POINT
Least-squares processHighest resolution: 7 Å

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