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- EMDB-43544: Rat GluN1-2B with Fab 003-102 -

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Basic information

Entry
Database: EMDB / ID: EMD-43544
TitleRat GluN1-2B with Fab 003-102
Map data
Sample
  • Complex: Rat GluN1-2B with Fab 003-102
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Protein or peptide: 003-102 Heavy
    • Protein or peptide: 003-102 Light
KeywordsChannel / heterotetramer / receptor / antibody / MEMBRANE PROTEIN
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 / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / positive regulation of Schwann cell migration / regulation of cell communication ...cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / positive regulation of Schwann cell migration / regulation of cell communication / auditory behavior / sensitization / olfactory learning / response to methylmercury / response to other organism / response to hydrogen sulfide / fear response / dendritic branch / conditioned taste aversion / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / apical dendrite / suckling behavior / transmitter-gated monoatomic ion channel activity / response to manganese ion / interleukin-1 receptor binding / response to carbohydrate / regulation of respiratory gaseous exchange / cellular response to lipid / propylene metabolic process / response to glycine / response to growth hormone / cellular response to dsRNA / RAF/MAP kinase cascade / negative regulation of dendritic spine maintenance / positive regulation of inhibitory postsynaptic potential / neurotransmitter receptor complex / heterocyclic compound binding / response to amine / Synaptic adhesion-like molecules / response to glycoside / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / neuromuscular process / ligand-gated sodium channel activity / regulation of axonogenesis / calcium ion transmembrane import into cytosol / response to morphine / positive regulation of glutamate secretion / male mating behavior / regulation of dendrite morphogenesis / protein heterotetramerization / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / small molecule binding / glycine binding / startle response / receptor clustering / parallel fiber to Purkinje cell synapse / regulation of neuronal synaptic plasticity / regulation of MAPK cascade / regulation of postsynaptic membrane potential / associative learning / behavioral response to pain / positive regulation of calcium ion transport into cytosol / extracellularly glutamate-gated ion channel activity / cellular response to glycine / response to electrical stimulus / positive regulation of dendritic spine maintenance / action potential / monoatomic cation transmembrane transport / multicellular organismal response to stress / response to magnesium ion / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / detection of mechanical stimulus involved in sensory perception of pain / monoatomic cation transport / glutamate receptor binding / response to mechanical stimulus / social behavior / ligand-gated monoatomic ion channel activity / behavioral fear response / prepulse inhibition / phosphatase binding / long-term memory / postsynaptic density, intracellular component / calcium ion homeostasis / synaptic cleft / response to fungicide / monoatomic cation channel activity / adult locomotory behavior / cellular response to manganese ion / glutamate-gated receptor activity / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic active zone membrane
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 speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsMichalski K / Furukawa H
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43544.png

Downloads & links

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Map

FileDownload / File: emd_43544.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342.4 Å		0.86 Å/pix.
x 400 pix.
= 342.4 Å		0.86 Å/pix.
x 400 pix.
= 342.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0575
Minimum - Maximum-0.592487 - 1.0092299
Average (Standard dev.)0.00025323618 (±0.01621532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43544_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_43544_half_map_2.map
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Sample components

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Entire : Rat GluN1-2B with Fab 003-102

EntireName: Rat GluN1-2B with Fab 003-102
Components
  • Complex: Rat GluN1-2B with Fab 003-102
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Protein or peptide: 003-102 Heavy
    • Protein or peptide: 003-102 Light

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Supramolecule #1: Rat GluN1-2B with Fab 003-102

SupramoleculeName: Rat GluN1-2B with Fab 003-102 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 91.944094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KIVNIGAVLS TRKHEQMFRE AVNQANKRHG SWKIQLQATS VTHKPNAIQM ALSVCEDLIS SQVYAILVSH PPTPNDHFTP TPVSYTAGF YRIPVLGLTT RMSIYSDKSI HLSFLRTVPP YSHQSSVWFE MMRVYNWNHI ILLVSDDHEG RAAQKRLETL L EERESKAE ...String:
KIVNIGAVLS TRKHEQMFRE AVNQANKRHG SWKIQLQATS VTHKPNAIQM ALSVCEDLIS SQVYAILVSH PPTPNDHFTP TPVSYTAGF YRIPVLGLTT RMSIYSDKSI HLSFLRTVPP YSHQSSVWFE MMRVYNWNHI ILLVSDDHEG RAAQKRLETL L EERESKAE KVLQFDPGTK NVTALLMEAR ELEARVIILS ASEDDAATVY RAAAMLDMTG SGYVWLVGER EISGNALRYA PD GIIGLQL INGKNESAHI SDAVGVVAQA VHELLEKENI TDPPRGCVGN TNIWKTGPLF KRVLMSSKYA DGVTGRVEFN EDG DRKFAQ YSIMNLQNRK LVQVGIYNGT HVIPNDRKII WPGGETEKPR GYQMSTRLKI VTIHQEPFVY VKPTMSDGTC KEEF TVNGD PVKKVICTGP NDTSPGSPRH TVPQCCYGFC IDLLIKLART MQFTYEVHLV ADGKFGTQER VQNSNKKEWN GMMGE LLSG QADMIVAPLT INNERAQYIE FSKPFKYQGL TILVKKEIPR STLDSFMNPF QSTLWLLVGL SVHVVAVMLY LLDRFS PFG RFKVNSEEEE EDALTLSSAM WFSWGVLLNS GIGEGAPRSF SARILGMVWA GFAMIIVASY TANLAAFLVL DRPEERI TG INDPRLRNPS DKFIYATVKQ SSVDIYFRRQ VELSTMYRHM EKHNYESAAE AIQAVRDNKL HAFIWDSAVL EFEASQKC D LVTTGELFFR SGFGIGMRKD SPWKQQVSLS ILKSHENGFM EDLDKTWVRY QECDSRSNAP ATLTFENMAG VFMIVAGGI VAGIFLIFIE IAYKSRA

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 91.269125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SIGIAVILVG TSDEVAIKDA HEKDDFHHLS VVPRVELVAM NETDPKSIIT RICDLMSDRK IQGVVFADDT DQEAIAQILD FISAQTLTP ILGIHGGSSM IMADKDESSM FFQFGPSIEQ QASVMLNIME EYDWYIFSIV TTYFPGYQDF VNKIRSTIEN S FVGWELEE ...String:
SIGIAVILVG TSDEVAIKDA HEKDDFHHLS VVPRVELVAM NETDPKSIIT RICDLMSDRK IQGVVFADDT DQEAIAQILD FISAQTLTP ILGIHGGSSM IMADKDESSM FFQFGPSIEQ QASVMLNIME EYDWYIFSIV TTYFPGYQDF VNKIRSTIEN S FVGWELEE VLLLDMSLDD GDSKIQNQLK KLQSPIILLY CTKEEATYIF EVANSVGLTG YGYTWIVPSL VAGDTDTVPS EF PTGLISV SYDEWDYGLP ARVRDGIAII TTAASDMLSE HSFIPEPKSS CYNTHEKRIY QSNMLNRYLI NVTFEGRDLS FSE EGYQMH PKLVIILLNK ERKWERVGKW KDKSLQMKYY VWPRMCPETE EQEDDHLSIV TLEEAPFVIV ESVDPLSGTC MRNT VPCEK RIISENKTDE EPGYIKKCCK GFCIDILKKI SKSVKFTYDL YLVTNGKHGK KINGTWNGMI GEVVMKRAYM AVGSL TINE ERSEVVDFSV PFIETGISVM VSRSNGTVSP SAFLEPFSAD VWVMMFVMLL IVSAVAVFVF EYFSPVGYNR CLADGR EPG GPSFTIGKAI WLLWGLVFNN SVPVQNPKGT TSKIMVSVWA FFAVIFLASY TANLAAFMIQ EEYVDQVSGL SDKKFQR PN DFSPPFRFGT VPNGSTERNI RNNYAEMHAY MGKFNQRGVD DALLSLKTGK LDAFIYDAAV LNYMAGRDEG CKLVTIGS G KVFASTGYGI AIQKDSGWKR QVDLAILQLF GDGEMEELEA LWLTGICHNE KNEVMSSQLD IDNMAGVFYM LGAAMALSL ITFISEHLFY WQ

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #3: 003-102 Heavy

MacromoleculeName: 003-102 Heavy / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.477862 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LQLQESGPGL VKPSQTLSLT CTVSGGSISS SNWWSWVRQP PGKGLEWIGE IYHSGNTNYN PSLKSRVTVS VDKSKNQFSL KLTSVTAAD TAVYYCARDV SGGVNWFDPW GQGTLV

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Macromolecule #4: 003-102 Light

MacromoleculeName: 003-102 Light / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.582475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NFMLTQPHSV SESPGKTVTI SCTRSSGSIA SNYVQWYQQR PGSAPTTVIY EDNQRPSGVP DRFSGSIDSS SNSASLTISG LKTEDEADY YCQSYDSSTV VFGGGTKLT

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 516895
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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