|Entry||Database: PDB / ID: 5iov|
|Title||Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine/Ro25-6981-bound conformation|
|Keywords||SIGNALING PROTEIN / ligand-gated ion channel / synaptic transmission|
|Function / homology||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 ...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 source||Xenopus laevis (African clawed frog)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.5 Å resolution|
|Authors||Zhu, S. / Stein, A.R. / Yoshioka, C. / Lee, C.H. / Goehring, A. / Mchaourab, S.H. / Gouaux, E.|
|Citation||Journal: 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.
SummaryFull reportAbout validation report
|Date||Deposition: Mar 9, 2016 / Release: Apr 20, 2016|
|Structure viewer||Molecule: |
Downloads & links
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
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
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||#4: Chemical||#5: Chemical|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: GluN1-GluN2B receptor in the complex with glycine and glutamate plus allosteric inhibitor Ro25-6981|
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1,
|Source (natural)||Organism: Xenopus laevis (African clawed frog)||Source (recombinant)||Organism: Homo sapiens (human) / Plasmid: Bacmam||Buffer solution||pH: 6.5||Specimen||Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES||Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 18 kelvins|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 0.01 mm|
|Image recording||Electron dose: 10.2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 186539|
|3D reconstruction||Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 87851 / Symmetry type: POINT|
|Least-squares process||Highest resolution: 7.5 Å|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi