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Yorodumi- EMDB-61622: Structure of native di-heteromeric GluN1-GluN2B NMDA receptor in ... -
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Basic information
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| Title | Structure of native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus | |||||||||
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Keywords | MEMBRANE PROTEIN / native NMDA receptor / adult rat cartex & hippocampus / GluN2A / GluN2B / MEMBRANE PROTEIN-IMMUNE SYSTEM complex | |||||||||
| Function / homology | Function and homology informationcellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / sensitization / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / sensitization / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / response to other organism / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / fear response / apical dendrite / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / suckling behavior / response to methylmercury / response to glycine / propylene metabolic process / response to manganese ion / response to carbohydrate / interleukin-1 receptor binding / cellular response to dsRNA / response to growth hormone / cellular response to lipid / negative regulation of dendritic spine maintenance / heterocyclic compound binding / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / positive regulation of glutamate secretion / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / voltage-gated monoatomic cation channel activity / response to glycoside / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / response to morphine / calcium ion transmembrane import into cytosol / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / glycine binding / regulation of synapse assembly / response to amine / regulation of cAMP/PKA signal transduction / small molecule binding / parallel fiber to Purkinje cell synapse / receptor clustering / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / behavioral response to pain / positive regulation of calcium ion transport into cytosol / regulation of MAPK cascade / response to magnesium ion / regulation of postsynaptic membrane potential / cellular response to glycine / associative learning / action potential / extracellularly glutamate-gated ion channel activity / excitatory synapse / monoatomic cation transport / positive regulation of dendritic spine maintenance / response to electrical stimulus / social behavior / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / glutamate receptor binding / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / response to mechanical stimulus / synaptic cleft / neuron development / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / prepulse inhibition / phosphatase binding / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / regulation of neuron apoptotic process / cell adhesion molecule binding / D2 dopamine receptor binding Similarity search - Function | |||||||||
| Biological species | ![]() ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Zhang M / Feng J / Li Y / Zhu S | |||||||||
| Funding support | China, 1 items
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Citation | Journal: Cell / Year: 2025Title: Assembly and architecture of endogenous NMDA receptors in adult cerebral cortex and hippocampus. Authors: Ming Zhang / Juan Feng / Chun Xie / Nan Song / Chaozhi Jin / Jian Wang / Qun Zhao / Lihua Zhang / Boshuang Wang / Yidi Sun / Fei Guo / Yang Li / Shujia Zhu / ![]() Abstract: The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). ...The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). However, subunit assembly and molecular architecture of endogenous NMDARs (eNMDARs) in the brain remain elusive. Using conformation- and subunit-dependent antibodies, we purified eNMDARs from adult rat cerebral cortex and hippocampus. Three major subtypes of GluN1-N2A-N2B, GluN1-N2B, and GluN1-N2A eNMDARs were resolved by cryoelectron microscopy (cryo-EM) at the resolution up to 4.2 Å. The particle ratio of these three subtypes was 9:7:4, indicating that about half of GluN2A and GluN2B subunits are incorporated into the tri-heterotetramers. Structural analysis revealed the asymmetric architecture of the GluN1-N2A-N2B receptor throughout the extracellular to the transmembrane layers. Moreover, the conformational variations between GluN1-N2B and GluN1-N2A-N2B receptors revealed the distinct biophysical properties across different eNMDAR subtypes. Our findings imply the structural and functional complexity of eNMDARs and shed light on structure-based therapeutic design targeting these eNMDARs in vivo. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_61622.map.gz | 117.8 MB | EMDB map data format | |
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| Header (meta data) | emd-61622-v30.xml emd-61622.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_61622_fsc.xml | 14.6 KB | Display | FSC data file |
| Images | emd_61622.png | 138.4 KB | ||
| Masks | emd_61622_msk_1.map | 125 MB | Mask map | |
| Filedesc metadata | emd-61622.cif.gz | 7.7 KB | ||
| Others | emd_61622_half_map_1.map.gz emd_61622_half_map_2.map.gz | 115.7 MB 115.7 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-61622 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-61622 | HTTPS FTP |
-Validation report
| Summary document | emd_61622_validation.pdf.gz | 990.9 KB | Display | EMDB validaton report |
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| Full document | emd_61622_full_validation.pdf.gz | 990.5 KB | Display | |
| Data in XML | emd_61622_validation.xml.gz | 18.5 KB | Display | |
| Data in CIF | emd_61622_validation.cif.gz | 24.4 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-61622 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-61622 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9jnnMC ![]() 8xljC ![]() 8xlkC ![]() 8xllC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_61622.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.071 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_61622_msk_1.map | ||||||||||||
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-Half map: #2
| File | emd_61622_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_61622_half_map_2.map | ||||||||||||
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Sample components
+Entire : Native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex an...
+Supramolecule #1: Native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex an...
+Supramolecule #2: NMDA receptor
+Supramolecule #3: Fab 4F11
+Supramolecule #4: Fab2
+Supramolecule #5: Fab
+Macromolecule #1: Glutamate receptor ionotropic, NMDA 1
+Macromolecule #2: Glutamate receptor ionotropic, NMDA 2B
+Macromolecule #3: Heavy Chain of GluN1 Fab, 4F11
+Macromolecule #4: Light Chain of GluN1 Fab, 4F11
+Macromolecule #5: Heavy Chain of GluN2B Fab2
+Macromolecule #6: Light Chain of GluN2B Fab2
+Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #10: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | tissue |
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Sample preparation
| Buffer | pH: 8 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TALOS ARCTICA |
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| Image recording | Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Average electron dose: 60.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
China, 1 items
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Trichoplusia ni (cabbage looper)

Processing
FIELD EMISSION GUN

