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Yorodumi- PDB-5up2: Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 5up2 | |||||||||
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Title | Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, Ro 25-6981, MK-801 and a GluN2B-specific Fab, at pH 6.5 | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / response to zinc ion / response to magnesium ion / glutamate-gated calcium ion channel activity / regulation of membrane potential / excitatory postsynaptic potential / long-term synaptic potentiation ...NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / response to zinc ion / response to magnesium ion / glutamate-gated calcium ion channel activity / 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 | Xenopus laevis (African clawed frog) Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å | |||||||||
Authors | Lu, W. / Du, J. / Goehring, A. / Gouaux, E. | |||||||||
Citation | Journal: Science / Year: 2017 Title: Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation. Authors: Wei Lü / Juan Du / April Goehring / Eric Gouaux / Abstract: -methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B ...-methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B receptor in the absence or presence of the GluN2B-specific allosteric modulator Ro 25-6981 (Ro), determined by cryogenic electron microscopy (cryo-EM). In the absence of Ro, the GluN2A and GluN2B amino-terminal domains (ATDs) adopt "closed" and "open" clefts, respectively. Upon binding Ro, the GluN2B ATD clamshell transitions from an open to a closed conformation. Consistent with a predominance of the GluN2A subunit in ion channel gating, the GluN2A subunit interacts more extensively with GluN1 subunits throughout the receptor, in comparison with the GluN2B subunit. Differences in the conformation of the pseudo-2-fold-related GluN1 subunits further reflect receptor asymmetry. The triheteromeric NMDAR structures provide the first view of the most common NMDA receptor assembly and show how incorporation of two different GluN2 subunits modifies receptor symmetry and subunit interactions, allowing each subunit to uniquely influence receptor structure and function, thus increasing receptor complexity. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5up2.cif.gz | 882.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5up2.ent.gz | 716.5 KB | Display | PDB format |
PDBx/mmJSON format | 5up2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5up2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5up2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5up2_validation.xml.gz | 117.7 KB | Display | |
Data in CIF | 5up2_validation.cif.gz | 173.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/5up2 ftp://data.pdbj.org/pub/pdb/validation_reports/up/5up2 | HTTPS FTP |
-Related structure data
Related structure data | 8581MC 8579C 8580C 8583C 5uowC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-N-methyl-D-aspartate receptor subunit ... , 2 types, 3 molecules ACB
#1: Protein | Mass: 94056.859 Da / Num. of mol.: 2 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 | | Mass: 93535.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC100127346 / Production host: Homo sapiens (human) / References: UniProt: B7ZSK1 |
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-Protein / Antibody , 2 types, 3 molecules DFG
#3: Protein | Mass: 94552.234 Da / Num. of mol.: 1 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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#4: Antibody | Mass: 18400.619 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
-Sugars , 2 types, 5 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #6: Sugar | ChemComp-NAG / | |
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-Details
Sequence details | Chain F and G is a GluN2B-specific Fab, termed 11D1. Sequence is unknown |
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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 |
-Sample preparation
Component | Name: membrane protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 0.84 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 302052 / Symmetry type: POINT |