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- PDB-8vvh: rat GluN1a-2B Fab 003-102 local refinement -

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Basic information

Entry
Database: PDB / ID: 8vvh
Titlerat GluN1a-2B Fab 003-102 local refinement
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 corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / auditory behavior / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors ...cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / auditory behavior / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / response to carbohydrate / fear response / sensitization / suckling behavior / olfactory learning / response to other organism / response to methylmercury / response to hydrogen sulfide / protein localization to postsynaptic membrane / dendritic branch / conditioned taste aversion / regulation of ARF protein signal transduction / apical dendrite / transmitter-gated monoatomic ion channel activity / response to manganese ion / response to glycoside / interleukin-1 receptor binding / cellular response to dsRNA / regulation of respiratory gaseous exchange / cellular response to lipid / propylene metabolic process / response to glycine / response to growth hormone / neuromuscular process / RAF/MAP kinase cascade / positive regulation of inhibitory postsynaptic potential / heterocyclic compound binding / negative regulation of dendritic spine maintenance / neurotransmitter receptor complex / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / regulation of axonogenesis / ligand-gated sodium channel activity / response to morphine / positive regulation of glutamate secretion / calcium ion transmembrane import into cytosol / regulation of synapse assembly / male mating behavior / positive regulation of reactive oxygen species biosynthetic process / startle response / protein heterotetramerization / regulation of dendrite morphogenesis / small molecule binding / glycine binding / receptor clustering / behavioral response to pain / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / behavioral fear response / social behavior / regulation of neuronal synaptic plasticity / associative learning / regulation of postsynaptic membrane potential / regulation of MAPK cascade / action potential / response to electrical stimulus / extracellularly glutamate-gated ion channel activity / neuron development / cellular response to glycine / multicellular organismal response to stress / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / detection of mechanical stimulus involved in sensory perception of pain / response to magnesium ion / response to mechanical stimulus / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transport / glutamate receptor binding / ligand-gated monoatomic ion channel activity / prepulse inhibition / long-term memory / calcium ion homeostasis / phosphatase binding / adult locomotory behavior / postsynaptic density, intracellular component / synaptic cleft / response to fungicide / monoatomic cation channel activity / cellular response to manganese ion / glutamate-gated receptor activity / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / sensory perception of pain / response to cytokine
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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / 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: 3.95 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 31, 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
H: 003-102 Heavy
L: 003-102 Light


Theoretical massNumber of molelcules
Total (without water)105,5164
Polymers105,5164
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: 41352.012 Da / Num. of mol.: 1
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: 40103.426 Da / Num. of mol.: 1
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.: 1
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.: 1
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 GluN1a-2B Fab 003-102 local refinement / 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: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 516895 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027020
ELECTRON MICROSCOPYf_angle_d0.5989591
ELECTRON MICROSCOPYf_dihedral_angle_d3.9061002
ELECTRON MICROSCOPYf_chiral_restr0.0431130
ELECTRON MICROSCOPYf_plane_restr0.0041230

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