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- EMDB-8104: Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV... -

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Basic information

Entry
Database: EMDB / ID: 8104
TitleCryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 5
Map data
SampleGluN1-GluN2B receptor in the complex with competitive antagonists DCKA and D-APV
  • N-methyl-D-aspartate receptor subunit NR1-8aNMDA receptor
  • Ionotropic glutamate receptor subunit NR2B
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
SourceXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / 14.1 Å resolution
AuthorsZhu S / Stein AR
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 ReportPDB-ID: 5ipt

SummaryFull reportAbout validation report
DateDeposition: Apr 7, 2016 / Header (metadata) release: Apr 20, 2016 / Map release: Apr 20, 2016 / Last update: Apr 27, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.052
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.052
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5ipt
  • Surface level: 0.052
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5ipt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8104.map.gz (map file in CCP4 format, 33938 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
191 pix
1.07 Å/pix.
= 204.37 Å
201 pix
1.07 Å/pix.
= 215.07 Å
221 pix
1.07 Å/pix.
= 236.47 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:0.052 (by author), 0.052 (movie #1):
Minimum - Maximum-0.05242955 - 0.15200984
Average (Standard dev.)0.006215829 (0.020292083)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions201221191
Origin000
Limit200220190
Spacing221201191
CellA: 236.47003 Å / B: 215.07004 Å / C: 204.37003 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z221201191
origin x/y/z0.0000.0000.000
length x/y/z236.470215.070204.370
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ329329329
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS221201191
D min/max/mean-0.0520.1520.006

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Supplemental data

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Sample components

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Entire GluN1-GluN2B receptor in the complex with competitive antagonists...

EntireName: GluN1-GluN2B receptor in the complex with competitive antagonists DCKA and D-APV
Number of components: 3

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Component #1: cellular-component, GluN1-GluN2B receptor in the complex with com...

Cellular-componentName: GluN1-GluN2B receptor in the complex with competitive antagonists DCKA and D-APV
Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pEGBacmam / Cell of expression system: GnTI-

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Component #2: protein, N-methyl-D-aspartate receptor subunit NR1-8a

ProteinName: N-methyl-D-aspartate receptor subunit NR1-8aNMDA receptor
Recombinant expression: No
MassTheoretical: 92.651234 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

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Component #3: protein, Ionotropic glutamate receptor subunit NR2B

ProteinName: Ionotropic glutamate receptor subunit NR2B / Recombinant expression: No
MassTheoretical: 93.234742 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/ml / pH: 6.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 18 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 10.5 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 32608
3D reconstructionSoftware: RELION / Resolution: 14.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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