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- EMDB-75123: SK3D-Germline in complex with GluN1-GluN2B, full refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-75123
TitleSK3D-Germline in complex with GluN1-GluN2B, full refinement
Map dataSK3D-Germline in complex with GluN1-GluN2B, full refinement
Sample
  • Complex: SK3D IgG in complex with GluN1-GluN2B NMDAR protein
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Protein or peptide: Light chain
    • Protein or peptide: Heavy chain
KeywordsNMDAR / antibody / SIGNALING PROTEIN / SIGNALING PROTEIN-Immune System complex
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / propylene metabolic process / response to glycine / negative regulation of dendritic spine maintenance / Assembly and cell surface presentation of NMDA receptors / neurotransmitter receptor complex / regulation of monoatomic cation transmembrane transport ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / propylene metabolic process / response to glycine / negative regulation of dendritic spine maintenance / Assembly and cell surface presentation of NMDA receptors / neurotransmitter receptor complex / regulation of monoatomic cation transmembrane transport / Neurexins and neuroligins / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / positive regulation of calcium ion transport into cytosol / Long-term potentiation / regulation of neuronal synaptic plasticity / monoatomic cation transport / ligand-gated monoatomic ion channel activity / synaptic cleft / calcium ion homeostasis / MECP2 regulates neuronal receptors and channels / positive regulation of synaptic transmission, glutamatergic / EPHB-mediated forward signaling / glutamate-gated calcium ion channel activity / excitatory synapse / ionotropic glutamate receptor signaling pathway / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of excitatory postsynaptic potential / sodium ion transmembrane transport / synaptic membrane / synaptic transmission, glutamatergic / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / brain development / regulation of synaptic plasticity / visual learning / postsynaptic density membrane / calcium ion transmembrane transport / terminal bouton / synaptic vesicle / long-term synaptic potentiation / late endosome / amyloid-beta binding / signaling receptor activity / RAF/MAP kinase cascade / dendritic spine / chemical synaptic transmission / response to ethanol / cytoskeleton / learning or memory / calmodulin binding / postsynaptic membrane / lysosome / neuron projection / postsynaptic density / 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
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 speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsKleeman SO / Furukawa HF
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
CitationJournal: To Be Published
Title: Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity
Authors: Kleeman SO / Furukawa HF
History
DepositionJan 15, 2026-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75123.png

Downloads & links

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Map

FileDownload / File: emd_75123.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSK3D-Germline in complex with GluN1-GluN2B, full refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 400 pix.
= 400. Å		1 Å/pix.
x 400 pix.
= 400. Å		1 Å/pix.
x 400 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.42364776 - 0.6713684
Average (Standard dev.)-0.000028714412 (±0.011734035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_75123_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_75123_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SK3D IgG in complex with GluN1-GluN2B NMDAR protein

EntireName: SK3D IgG in complex with GluN1-GluN2B NMDAR protein
Components
  • Complex: SK3D IgG in complex with GluN1-GluN2B NMDAR protein
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Protein or peptide: Light chain
    • Protein or peptide: Heavy chain

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Supramolecule #1: SK3D IgG in complex with GluN1-GluN2B NMDAR protein

SupramoleculeName: SK3D IgG in complex with GluN1-GluN2B NMDAR protein / 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: Homo sapiens (human)
Molecular weightTheoretical: 94.854508 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTMHLLTFA LLFSCSFARA ASDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYS W NHIILLVS ...String:
MSTMHLLTFA LLFSCSFARA ASDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYS W NHIILLVS DDHEGRAAQK RLETLLEERE SKAEKVLQFD PGTKNVTALL MEARELEARV IILSASEDDA ATVYRAAAML NM TGSGYVW LVGEREISGN ALRYAPDGII GLQLINGKNE SAHISDAVGV VAQAVHELLE KENITDPPRG CVGNTNIWKT GPL FKRVLM SSKYADGVTG RVEFNEDGDR KFANYSIMNL QNRKLVQVGI YNGTHVIPND RKIIWPGGET EKPRGYQMST RLKI VTIHQ EPFVYVKPTL SDGTCKEEFT VNGDPVKKVI CTGPNDTSPG SPRHTVPQCC YGFCIDLLIK LARTMNFTYE VHLVA DGKF GTQERVNNSN KKEWNGMMGE LLSGQADMIV APLTINNERA QYIEFSKPFK YQGLTILVKK EIPRSTLDSF MNPFQS TLW LLVGLSVHVV AVMLYLLDRF SPFGRFKVNS EEEEEDALTL SSAMWFSWGV LLNSGIGEGA PRSFSARILG MVWAGFA MI IVASYTANLA AFLVLDRPEE RITGINDPRL RNPSDKFIYA TVKQSSVDIY FRRQVELSTM YRHMEKHNYE SAAEAIQA V RDNKLHAFIW DSAVLEFEAS QKCDLVTTGE LFFRSGFGIG MRKDSPWKQN VSLSILKSHE NGFMEDLDKT WVRYQECDS RSNAPATLTF ENMAGVFMIV AGGIVAGIFL IFIEIAYKRH KSRA

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: Homo sapiens (human)
Molecular weightTheoretical: 92.885961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: RSQKSPPSIG IAVILVGTSD EVAIKDAHEK DDFHHLSVVP RVELVAMNET DPKSIITRIC DLMSDRKIQG VVFADDTDQE AIAQILDFI SAQTLTPILG IHGGSSMIMA DKDESSMFFQ FGPSIEQQAS VMLNIMEEYD WYIFSIVTTY FPGYQDFVNK I RSTIENSF ...String:
RSQKSPPSIG IAVILVGTSD EVAIKDAHEK DDFHHLSVVP RVELVAMNET DPKSIITRIC DLMSDRKIQG VVFADDTDQE AIAQILDFI SAQTLTPILG IHGGSSMIMA DKDESSMFFQ FGPSIEQQAS VMLNIMEEYD WYIFSIVTTY FPGYQDFVNK I RSTIENSF VGWELEEVLL LDMSLDDGDS KIQNQLKKLQ SPIILLYCTK EEATYIFEVA NSVGLTGYGY TWIVPSLVAG DT DTVPSEF PTGLISVSYD EWDYGLPARV RDGIAIITTA ASDMLSEHSF IPEPKSSCYN THEKRIYQSN MLNRYLINVT FEG RNLSFS EDGYQMHPKL VIILLNKERK WERVGKWKDK SLQMKYYVWP RMCPETEEQE DDHLSIVTLE EAPFVIVESV DPLS GTCMR NTVPCEKRIV TENKTDEEPG YIKKCCKGFC IDILKKISKS VKFTYDLYLV TNGKHGKKIN GTWNGMIGEV VMKRA YMAV GSLTINEERS EVVDFSVPFI ETGISVMVSR SNGTVSPSAF LEPFSADVWV MMFVMLLIVS AVAVFVFEYF SPVGYN RSL ADGREPGGPS FTIGKAIWLL WGLVFNNSVP VQNPKGTTSK IMVSVWAFFA VIFLASYTAN LAAFMIQEEY VDQVSGL SD KKFQRPNDFS PPFRFGTVPN GSTERNIRNN YAEMHAYMGK FNQRGVDDAL LSLKTGKLDA FIYDAAVLNY MAGRDEGC K LVTIGSGKVF ASTGYGIAIQ KDSGWKRQVD LAILQLFGDG EMEELEALWL TGICHNEKNE VMSSQLDIDN MAGVFYMLG AAMALSLITF ISEHLFYWQF RHSFMG

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #3: Light chain

MacromoleculeName: Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.058446 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVLTQSPAS LAVSLGQRAT ISCRASKSVS TSGYSYMHWY QQKPGQPPKL LIYLASNLES GVPARFSGSG SGTDFTLNIH PVEEEDAAT YYCQHSRELP YTFGGGTKLE IK

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Macromolecule #4: Heavy chain

MacromoleculeName: Heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.258796 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EFQLQQSGPE LVKPGASVKM SCKASGYTFT SYVMHWVKQK PGQGLEWIGY IYPYNDGTKY NEKFKGKATL TSDKSSSTAY MELSSLTSE DSAVYYCARL TTVVEGAMDY WGQGTSVTVS S

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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

Concentration5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 71.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7saa

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 66165
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER / Details: cryoSPARC refinement

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