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Yorodumi- PDB-8jj2: Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 ... -
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-Basic information
Entry | Database: PDB / ID: 8jj2 | ||||||||||||||||||
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Title | Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in one fab conformation | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / NMDAR / autoimmune encephalitis | ||||||||||||||||||
Function / homology | Function and homology information excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / Assembly and cell surface presentation of NMDA receptors ...excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / glutamate receptor signaling pathway / NMDA glutamate receptor activity / Neurexins and neuroligins / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / glutamate binding / protein heterotetramerization / positive regulation of reactive oxygen species biosynthetic process / positive regulation of calcium ion transport into cytosol / glycine binding / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / startle response / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / monoatomic cation transport / Long-term potentiation / ligand-gated monoatomic ion channel activity / positive regulation of excitatory postsynaptic potential / excitatory synapse / calcium ion homeostasis / MECP2 regulates neuronal receptors and channels / synaptic cleft / glutamate-gated calcium ion channel activity / sensory perception of pain / EPHB-mediated forward signaling / Ras activation upon Ca2+ influx through NMDA receptor / response to amphetamine / ionotropic glutamate receptor signaling pathway / neurogenesis / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / long-term synaptic potentiation / postsynaptic density membrane / negative regulation of protein catabolic process / visual learning / cytoplasmic vesicle membrane / protein catabolic process / brain development / regulation of synaptic plasticity / terminal bouton / memory / response to wounding / synaptic vesicle / signaling receptor activity / presynaptic membrane / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / postsynaptic density / learning or memory / calmodulin binding / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / glutamatergic synapse / calcium ion binding / dendrite / synapse / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||||||||
Authors | Wang, H. / Zhu, S. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis. Authors: Han Wang / Chun Xie / Bo Deng / Jingjun Ding / Na Li / Zengwei Kou / Mengmeng Jin / Jie He / Qinrui Wang / Han Wen / Jinbao Zhang / Qinming Zhou / Sheng Chen / Xiangjun Chen / Ti-Fei Yuan / Shujia Zhu / Abstract: Antibodies against N-methyl-D-aspartate receptors (NMDARs) are most frequently detected in persons with autoimmune encephalitis (AE) and used as diagnostic biomarkers. Elucidating the structural ...Antibodies against N-methyl-D-aspartate receptors (NMDARs) are most frequently detected in persons with autoimmune encephalitis (AE) and used as diagnostic biomarkers. Elucidating the structural basis of monoclonal antibody (mAb) binding to NMDARs would facilitate the development of targeted therapy for AE. Here, we reconstructed nanodiscs containing green fluorescent protein-fused NMDARs to label and sort individual immune B cells from persons with AE and further cloned and identified mAbs against NMDARs. This allowed cryo-electron microscopy analysis of NMDAR-Fab complexes, revealing that autoantibodies bind to the R1 lobe of the N-terminal domain of the GluN1 subunit. Small-angle X-ray scattering studies demonstrated NMDAR-mAb stoichiometry of 2:1 or 1:2, structurally suitable for mAb-induced clustering and endocytosis of NMDARs. Importantly, these mAbs reduced the surface NMDARs and NMDAR-mediated currents, without tonically affecting NMDAR channel gating. These structural and functional findings imply that the design of neutralizing antibody binding to the R1 lobe of NMDARs represents a potential therapy for AE treatment. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jj2.cif.gz | 695.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jj2.ent.gz | 474.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jj2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8jj2_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8jj2_validation.xml.gz | 94.4 KB | Display | |
Data in CIF | 8jj2_validation.cif.gz | 140 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/8jj2 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/8jj2 | HTTPS FTP |
-Related structure data
Related structure data | 36338MC 8jizC 8jj0C 8jj1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Glutamate receptor ionotropic, NMDA ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 94136.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2A, NMDAR2A / Production host: Homo sapiens (human) / References: UniProt: Q12879 #2: Protein | Mass: 95236.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Homo sapiens (human) / References: UniProt: Q05586 |
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-Antibody , 2 types, 2 molecules EF
#3: Antibody | Mass: 26893.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#4: Antibody | Mass: 25764.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Sugars , 2 types, 9 molecules
#5: 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 |
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#6: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | Y |
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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: Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab28 Type: CELL / Entity ID: #1-#4 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | 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: 281 K |
-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 / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148340 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 169.6 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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