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- PDB-8vuy: Rat GluN1-2B with Fab 003-102 -

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Basic information

Entry
Database: PDB / ID: 8vuy
TitleRat GluN1-2B with Fab 003-102
Components
  • 003-102 Heavy
  • 003-102 Light
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2B
KeywordsMEMBRANE PROTEIN / Channel / heterotetramer / receptor / antibody
Function / homology
Function and homology information


cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / positive regulation of Schwann cell migration / pons maturation / sensitization / regulation of cell communication / 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 / positive regulation of Schwann cell migration / pons maturation / sensitization / regulation of cell communication / 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 / response to other organism / regulation of respiratory gaseous exchange / apical dendrite / fear response / regulation of ARF protein signal transduction / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / response to methylmercury / suckling behavior / response to manganese ion / response to glycine / interleukin-1 receptor binding / response to carbohydrate / propylene metabolic process / cellular response to dsRNA / cellular response to lipid / response to growth hormone / heterocyclic compound binding / negative regulation of dendritic spine maintenance / positive regulation of glutamate secretion / RAF/MAP kinase cascade / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / 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 / regulation of axonogenesis / neuromuscular process / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / response to amine / regulation of cAMP/PKA signal transduction / receptor clustering / small molecule binding / startle response / parallel fiber to Purkinje cell synapse / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / behavioral response to pain / regulation of MAPK cascade / positive regulation of calcium ion transport into cytosol / cellular response to glycine / extracellularly glutamate-gated ion channel activity / regulation of postsynaptic membrane potential / response to magnesium ion / action potential / associative learning / response to electrical stimulus / excitatory synapse / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / social behavior / monoatomic cation transport / regulation of neuronal synaptic plasticity / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / detection of mechanical stimulus involved in sensory perception of pain / long-term memory / response to mechanical stimulus / neuron development / synaptic cleft / phosphatase binding / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / calcium ion homeostasis / glutamate-gated receptor activity / regulation of long-term synaptic depression / cell adhesion molecule binding / regulation of neuron apoptotic process
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsMichalski, K. / Furukawa, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NS11745, MH085926, F32MH121061, NS113632 United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural and functional mechanisms of anti-NMDAR autoimmune encephalitis.
Authors: Kevin Michalski / Taha Abdulla / Sam Kleeman / Lars Schmidl / Ricardo Gómez / Noriko Simorowski / Francesca Vallese / Harald Prüss / Manfred Heckmann / Christian Geis / Hiro Furukawa /
Abstract: Autoantibodies against neuronal membrane proteins can manifest in autoimmune encephalitis, inducing seizures, cognitive dysfunction and psychosis. Anti-N-methyl-D-aspartate receptor (NMDAR) ...Autoantibodies against neuronal membrane proteins can manifest in autoimmune encephalitis, inducing seizures, cognitive dysfunction and psychosis. Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is the most dominant autoimmune encephalitis; however, insights into how autoantibodies recognize and alter receptor functions remain limited. Here we determined structures of human and rat NMDARs bound to three distinct patient-derived antibodies using single-particle electron cryo-microscopy. These antibodies bind different regions within the amino-terminal domain of the GluN1 subunit. Through electrophysiology, we show that all three autoantibodies acutely and directly reduced NMDAR channel functions in primary neurons. Antibodies show different stoichiometry of binding and antibody-receptor complex formation, which in one antibody, 003-102, also results in reduced synaptic localization of NMDARs. These studies demonstrate mechanisms of diverse epitope recognition and direct channel regulation of anti-NMDAR autoantibodies underlying autoimmune encephalitis.
History
DepositionJan 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
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Revision 1.1Sep 18, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2B
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 2B
H: 003-102 Heavy
J: 003-102 Heavy
K: 003-102 Light
L: 003-102 Light


Theoretical massNumber of molelcules
Total (without water)414,5478
Polymers414,5478
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 91944.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / ...GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NMDAR2B / NR2B


Mass: 91269.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00960
#3: Antibody 003-102 Heavy


Mass: 12477.862 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody 003-102 Light


Mass: 11582.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rat GluN1-2B with Fab 003-102 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 516895 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00326212
ELECTRON MICROSCOPYf_angle_d0.59935804
ELECTRON MICROSCOPYf_dihedral_angle_d3.8893819
ELECTRON MICROSCOPYf_chiral_restr0.0434169
ELECTRON MICROSCOPYf_plane_restr0.0044607

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