+Open data
-Basic information
Entry | Database: PDB / ID: 6cna | ||||||||||||
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Title | GluN1-GluN2B NMDA receptors with exon 5 | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Splicing variant | ||||||||||||
Function / homology | Function and homology information neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration ...neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / regulation of protein kinase A signaling / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / apical dendrite / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / fear response / response to methylmercury / voltage-gated monoatomic cation channel activity / positive regulation of cysteine-type endopeptidase activity / cellular response to dsRNA / response to carbohydrate / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / interleukin-1 receptor binding / cellular response to lipid / response to morphine / NMDA glutamate receptor activity / positive regulation of glutamate secretion / response to growth hormone / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / response to manganese ion / NMDA selective glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / neuromuscular process / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / regulation of axonogenesis / male mating behavior / heterocyclic compound binding / suckling behavior / startle response / behavioral response to pain / response to amine / monoatomic cation transmembrane transport / receptor clustering / monoatomic cation transport / regulation of neuronal synaptic plasticity / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / regulation of MAPK cascade / response to magnesium ion / ligand-gated monoatomic ion channel activity / cellular response to organic cyclic compound / extracellularly glutamate-gated ion channel activity / cellular response to glycine / excitatory synapse / positive regulation of dendritic spine maintenance / neuron development / Unblocking of NMDA receptors, glutamate binding and activation / behavioral fear response / phosphatase binding / regulation of postsynaptic membrane potential / small molecule binding / postsynaptic density, intracellular component / cellular response to manganese ion / calcium ion homeostasis / glutamate receptor binding / D2 dopamine receptor binding / prepulse inhibition / multicellular organismal response to stress / monoatomic cation channel activity / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / regulation of neuron apoptotic process / response to electrical stimulus / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||||||||
Authors | Furukawa, H. / Grant, T. / Grigorieff, N. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Neuron / Year: 2018 Title: Structural Mechanism of Functional Modulation by Gene Splicing in NMDA Receptors. Authors: Michael C Regan / Timothy Grant / Miranda J McDaniel / Erkan Karakas / Jing Zhang / Stephen F Traynelis / Nikolaus Grigorieff / Hiro Furukawa / Abstract: Alternative gene splicing gives rise to N-methyl-D-aspartate (NMDA) receptor ion channels with defined functional properties and unique contributions to calcium signaling in a given chemical ...Alternative gene splicing gives rise to N-methyl-D-aspartate (NMDA) receptor ion channels with defined functional properties and unique contributions to calcium signaling in a given chemical environment in the mammalian brain. Splice variants possessing the exon-5-encoded motif at the amino-terminal domain (ATD) of the GluN1 subunit are known to display robustly altered deactivation rates and pH sensitivity, but the underlying mechanism for this functional modification is largely unknown. Here, we show through cryoelectron microscopy (cryo-EM) that the presence of the exon 5 motif in GluN1 alters the local architecture of heterotetrameric GluN1-GluN2 NMDA receptors and creates contacts with the ligand-binding domains (LBDs) of the GluN1 and GluN2 subunits, which are absent in NMDA receptors lacking the exon 5 motif. The unique interactions established by the exon 5 motif are essential to the stability of the ATD/LBD and LBD/LBD interfaces that are critically involved in controlling proton sensitivity and deactivation. | ||||||||||||
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 | 6cna.cif.gz | 573 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cna.ent.gz | 443.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cna_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6cna_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6cna_validation.xml.gz | 92.2 KB | Display | |
Data in CIF | 6cna_validation.cif.gz | 139.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/6cna ftp://data.pdbj.org/pub/pdb/validation_reports/cn/6cna | HTTPS FTP |
-Related structure data
Related structure data | 7529MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 94455.906 Da / Num. of mol.: 2 / Fragment: residues 25-859 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 Production host: Spodoptera frugiperda multiple nucleopolyhedrovirus References: UniProt: P35439 #2: Protein | Mass: 91160.156 Da / Num. of mol.: 2 / Fragment: residues 34-843 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b Production host: Spodoptera frugiperda multiple nucleopolyhedrovirus References: UniProt: Q00960 #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Buffer component | Conc.: 20 mM / Name: HEPES | ||||||||||||||||||||||||
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: 96 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10_2155: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73790 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 4.6 Å | ||||||||||||||||||||||||
Refine LS restraints |
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