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- EMDB-38451: Structure of native tri-heteromeric GluN1-GluN2A-GluN2B NMDA rece... -

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Basic information

Entry
Database: EMDB / ID: EMD-38451
TitleStructure of native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat cortex and hippocampus
Map data
Sample
  • Tissue: Native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat cortex and hippocampus
    • Complex: NMDA receptor
      • Protein or peptide: x 3 types
    • Complex: Fab
      • Complex: Fab 4F11
        • Protein or peptide: x 2 types
      • Complex: Fab 28C
        • Protein or peptide: x 2 types
      • Complex: Fab2
        • Protein or peptide: x 2 types
  • Ligand: x 2 types
KeywordsMEMBRANE PROTEIN / native NMDA receptor / adult rat cartex & hippocampus / GluN2A / GluN2B / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / cellular response to curcumin / cellular response to corticosterone stimulus / receptor recycling / cellular response to magnesium starvation / sensory organ development / directional locomotion / pons maturation ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / cellular response to curcumin / cellular response to corticosterone stimulus / receptor recycling / cellular response to magnesium starvation / sensory organ development / directional locomotion / pons maturation / response to environmental enrichment / positive regulation of Schwann cell migration / regulation of cell communication / sensitization / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / auditory behavior / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / olfactory learning / conditioned taste aversion / dendritic branch / response to hydrogen sulfide / regulation of respiratory gaseous exchange / response to other organism / positive regulation of inhibitory postsynaptic potential / protein localization to postsynaptic membrane / cellular response to magnesium ion / apical dendrite / regulation of ARF protein signal transduction / response to methylmercury / fear response / transmitter-gated monoatomic ion channel activity / conditioned place preference / locomotion / response to glycine / propylene metabolic process / dendritic spine organization / response to carbohydrate / regulation of NMDA receptor activity / sleep / cellular response to dsRNA / interleukin-1 receptor binding / negative regulation of dendritic spine maintenance / cellular response to lipid / positive regulation of glutamate secretion / response to growth hormone / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / response to manganese ion / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / cellular response to zinc ion / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / glutamate receptor signaling pathway / glutamate binding / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / regulation of synapse assembly / male mating behavior / heterocyclic compound binding / glycine binding / spinal cord development / positive regulation of reactive oxygen species biosynthetic process / receptor clustering / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / suckling behavior / regulation of postsynaptic membrane potential / response to amine / small molecule binding / startle response / dopamine metabolic process / social behavior / monoatomic cation transmembrane transport / response to lithium ion / associative learning / modulation of excitatory postsynaptic potential / : / behavioral response to pain / response to magnesium ion / regulation of MAPK cascade / regulation of neuronal synaptic plasticity / action potential / cellular response to glycine / extracellularly glutamate-gated ion channel activity / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / response to light stimulus / positive regulation of protein targeting to membrane / positive regulation of dendritic spine maintenance / monoatomic ion channel complex
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 2A / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculoides (Temminck's mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsZhang M / Feng J / Li Y / Zhu S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Cell / Year: 2025
Title: Assembly and architecture of endogenous NMDA receptors in adult cerebral cortex and hippocampus.
Authors: Ming Zhang / Juan Feng / Chun Xie / Nan Song / Chaozhi Jin / Jian Wang / Qun Zhao / Lihua Zhang / Boshuang Wang / Yidi Sun / Fei Guo / Yang Li / Shujia Zhu /
Abstract: The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). ...The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). However, subunit assembly and molecular architecture of endogenous NMDARs (eNMDARs) in the brain remain elusive. Using conformation- and subunit-dependent antibodies, we purified eNMDARs from adult rat cerebral cortex and hippocampus. Three major subtypes of GluN1-N2A-N2B, GluN1-N2B, and GluN1-N2A eNMDARs were resolved by cryoelectron microscopy (cryo-EM) at the resolution up to 4.2 Å. The particle ratio of these three subtypes was 9:7:4, indicating that about half of GluN2A and GluN2B subunits are incorporated into the tri-heterotetramers. Structural analysis revealed the asymmetric architecture of the GluN1-N2A-N2B receptor throughout the extracellular to the transmembrane layers. Moreover, the conformational variations between GluN1-N2B and GluN1-N2A-N2B receptors revealed the distinct biophysical properties across different eNMDAR subtypes. Our findings imply the structural and functional complexity of eNMDARs and shed light on structure-based therapeutic design targeting these eNMDARs in vivo.
History
DepositionDec 26, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_38451.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.72 Å
1.07 Å/pix.
x 320 pix.
= 342.72 Å
1.07 Å/pix.
x 320 pix.
= 342.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-20.121500000000001 - 29.939879999999999
Average (Standard dev.)0.000000000002699 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38451_msk_1.map
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Half map: #1

Fileemd_38451_half_map_1.map
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Half map: #2

Fileemd_38451_half_map_2.map
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Sample components

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Entire : Native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat c...

EntireName: Native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat cortex and hippocampus
Components
  • Tissue: Native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat cortex and hippocampus
    • Complex: NMDA receptor
      • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
      • Protein or peptide: Glutamate receptor ionotropic, NMDA 2A
      • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Complex: Fab
      • Complex: Fab 4F11
        • Protein or peptide: Heavy Chain of GluN1 Fab, 4F11
        • Protein or peptide: Light Chain of GluN1 Fab, 4F11
      • Complex: Fab 28C
        • Protein or peptide: Heavy Chain of GluN2A Fab, 28C
        • Protein or peptide: Light Chain of GluN2A Fab, 28C
      • Complex: Fab2
        • Protein or peptide: Heavy Chain of GluN2B Fab2
        • Protein or peptide: Light Chain of GluN2B Fab2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid

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Supramolecule #1: Native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat c...

SupramoleculeName: Native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat cortex and hippocampus
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #2: NMDA receptor

SupramoleculeName: NMDA receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3

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Supramolecule #3: Fab 4F11

SupramoleculeName: Fab 4F11 / type: complex / ID: 3 / Parent: 6 / Macromolecule list: #4-#5

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Supramolecule #4: Fab 28C

SupramoleculeName: Fab 28C / type: complex / ID: 4 / Parent: 6 / Macromolecule list: #6-#7

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Supramolecule #5: Fab2

SupramoleculeName: Fab2 / type: complex / ID: 5 / Parent: 6 / Macromolecule list: #8-#9

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Supramolecule #6: Fab

SupramoleculeName: Fab / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #4-#9
Source (natural)Organism: Mus musculoides (Temminck's mouse)

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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) / Strain: Wistar
Molecular weightTheoretical: 105.645875 KDa
SequenceString: MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS ...String:
MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN 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 EPFVYVKPTM SDGTCKEEFT VNGDPVKKVI CTGPNDTSPG SPRHTVPQCC YGFCIDLLIK LARTMNFTYE VHLVA DGKF GTQERVNNSN KKEWNGMMGE LLSGQADMIV APLTINNERA QYIEFSKPFK YQGLTILVKK EIPRSTLDSF MQPFQS 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 ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDARRKQMQL AFAAVNVWRK NLQDRKSGRA EPDPKKKATF RAITSTLAS SFKRRRSSKD TSTGGGRGAL QNQKDTVLPR RAIEREEGQL QLCSRHRES

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 2A

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Wistar
Molecular weightTheoretical: 165.666953 KDa
SequenceString: MGRLGYWTLL VLPALLVWRD PAQNAAAEKG PPALNIAVLL GHSHDVTERE LRNLWGPEQA TGLPLDVNVV ALLMNRTDPK SLITHVCDL MSGARIHGLV FGDDTDQEAV AQMLDFISSQ TFIPILGIHG GASMIMADKD PTSTFFQFGA SIQQQATVML K IMQDYDWH ...String:
MGRLGYWTLL VLPALLVWRD PAQNAAAEKG PPALNIAVLL GHSHDVTERE LRNLWGPEQA TGLPLDVNVV ALLMNRTDPK SLITHVCDL MSGARIHGLV FGDDTDQEAV AQMLDFISSQ TFIPILGIHG GASMIMADKD PTSTFFQFGA SIQQQATVML K IMQDYDWH VFSLVTTIFP GYRDFISFIK TTVDNSFVGW DMQNVITLDT SFEDAKTQVQ LKKIHSSVIL LYCSKDEAVL IL SEARSLG LTGYDFFWIV PSLVSGNTEL IPKEFPSGLI SVSYDDWDYS LEARVRDGLG ILTTAASSML EKFSYIPEAK ASC YGQAEK PETPLHTLHQ FMVNVTWDGK DLSFTEEGYQ VHPRLVVIVL NKDREWEKVG KWENQTLSLR HAVWPRYKSF SDCE PDDNH LSIVTLEEAP FVIVEDIDPL TETCVRNTVP CRKFVKINNS TNEGMNVKKC CKGFCIDILK KLSRTVKFTY DLYLV TNGK HGKKVNNVWN GMIGEVVYQR AVMAVGSLTI NEERSEVVDF SVPFVETGIS VMVSRSNGTV SPSAFLEPFS ASVWVM MFV MLLIVSAIAV FVFEYFSPVG YNRNLAKGKA PHGPSFTIGK AIWLLWGLVF NNSVPVQNPK GTTSKIMVSV WAFFAVI FL ASYTANLAAF MIQEEFVDQV TGLSDKKFQR PHDYSPPFRF GTVPNGSTER NIRNNYPYMH QYMTRFNQRG VEDALVSL K TGKLDAFIYD AAVLNYKAGR DEGCKLVTIG SGYIFASTGY GIALQKGSPW KRQIDLALLQ FVGDGEMEEL ETLWLTGIC HNEKNEVMSS QLDIDNMAGV FYMLAAAMAL SLITFIWEHL FYWKLRFCFT GVCSDRPGLL FSISRGIYSC IHGVHIEEKK KSPDFNLTG SQSNMLKLLR SAKNISNMSN MNSSRMDSPK RATDFIQRGS LIVDMVSDKG NLIYSDNRSF QGKDSIFGDN M NELQTFVA NRHKDNLSNY VFQGQHPLTL NESNPNTVEV AVSTESKGNS RPRQLWKKSM ESLRQDSLNQ NPVSQRDEKT AE NRTHSLK SPRYLPEEVA HSDISETSSR ATCHREPDNN KNHKTKDNFK RSMASKYPKD CSDVDRTYMK TKASSPRDKI YTI DGEKEP SFHLDPPQFV ENITLPENVG FPDTYQDHNE NFRKGDSTLP MNRNPLHNED GLPNNDQYKL YAKHFTLKDK GSPH SEGSD RYRQNSTHCR SCLSNLPTYS GHFTMRSPFK CDACLRMGNL YDIDEDQMLQ ETGNPATREE VYQQDWSQNN ALQFQ KNKL RINRQHSYDN ILDKPREIDL SRPSRSISLK DRERLLEGNL YGSLFSVPSS KLLGNKSSLF PQGLEDSKRS KSLLPD HAS DNPFLHTYGD DQRLVIGRCP SDPYKHSLPS QAVNDSYLRS SLRSTASYCS RDSRGHSDVY ISEHVMPYAA NKNTMYS TP RVLNSCSNRR VYKKMPSIES DV

UniProtKB: Glutamate receptor ionotropic, NMDA 2A

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Macromolecule #3: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Wistar
Molecular weightTheoretical: 166.274219 KDa
SequenceString: MKPSAECCSP KFWLVLAVLA VSGSKARSQK SPPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPKS IITRICDLM SDRKIQGVVF ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS IEQQASVMLN I MEEYDWYI ...String:
MKPSAECCSP KFWLVLAVLA VSGSKARSQK SPPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPKS IITRICDLM SDRKIQGVVF ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS IEQQASVMLN I MEEYDWYI FSIVTTYFPG YQDFVNKIRS TIENSFVGWE LEEVLLLDMS LDDGDSKIQN QLKKLQSPII LLYCTKEEAT YI FEVANSV GLTGYGYTWI VPSLVAGDTD TVPSEFPTGL ISVSYDEWDY GLPARVRDGI AIITTAASDM LSEHSFIPEP KSS CYNTHE KRIYQSNMLN RYLINVTFEG RNLSFSEDGY QMHPKLVIIL LNKERKWERV GKWKDKSLQM KYYVWPRMCP ETEE QEDDH LSIVTLEEAP FVIVESVDPL SGTCMRNTVP CQKRIISENK TDEEPGYIKK CCKGFCIDIL KKISKSVKFT YDLYL VTNG KHGKKINGTW NGMIGEVVMK RAYMAVGSLT INEERSEVVD FSVPFIETGI SVMVSRSNGT VSPSAFLEPF SADVWV MMF VMLLIVSAVA VFVFEYFSPV GYNRCLADGR EPGGPSFTIG KAIWLLWGLV FNNSVPVQNP KGTTSKIMVS VWAFFAV IF LASYTANLAA FMIQEEYVDQ VSGLSDKKFQ RPNDFSPPFR FGTVPNGSTE RNIRNNYAEM HAYMGKFNQR GVDDALLS L KTGKLDAFIY DAAVLNYMAG RDEGCKLVTI GSGKVFASTG YGIAIQKDSG WKRQVDLAIL QLFGDGEMEE LEALWLTGI CHNEKNEVMS SQLDIDNMAG VFYMLGAAMA LSLITFICEH LFYWQFRHCF MGVCSGKPGM VFSISRGIYS CIHGVAIEER QSVMNSPTA TMNNTHSNIL RLLRTAKNMA NLSGVNGSPQ SALDFIRRES SVYDISEHRR SFTHSDCKSY NNPPCEENLF S DYISEVER TFGNLQLKDS NVYQDHYHHH HRPHSIGSTS SIDGLYDCDN PPFTTQPRSI SKKPLDIGLP SSKHSQLSDL YG KFSFKSD RYSGHDDLIR SDVSDISTHT VTYGNIEGNA AKRRKQQYKD SLKKRPASAK SRREFDEIEL AYRRRPPRSP DHK RYFRDK EGLRDFYLDQ FRTKENSPHW EHVDLTDIYK ERSDDFKRDS VSGGGPCTNR SHLKHGTGEK HGVVGGVPAP WEKN LTNVD WEDRSGGNFC RSCPSKLHNY SSTVAGQNSG RQACIRCEAC KKAGNLYDIS EDNSLQELDQ PAAPVAVTSN ASSTK YPQS PTNSKAQKKN RNKLRRQHSY DTFVDLQKEE AALAPRSVSL KDKGRFMDGS PYAHMFEMPA GESSFANKSS VPTAGH HHN NPGSGYMLSK SLYPDRVTQN PFIPTFGDDQ CLLHGSKSYF FRQPTVAGAS KTRPDFRALV TNKPVVVTLH GAVPGRF QK DICIGNQSNP CVPNNKNPRA FNGSSNGHVY EKLSSIESDV

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #4: Heavy Chain of GluN1 Fab, 4F11

MacromoleculeName: Heavy Chain of GluN1 Fab, 4F11 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculoides (Temminck's mouse)
Molecular weightTheoretical: 15.536409 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
PMVSAIVLYV LLAAAAHSAF AMDVQLQESG PGLVKPSQSL SLTCTVTGYS ITSDYAWNWI RQFPGNKLEW MGYISYSGST GYNPSLKSR ISITRDTSKN QFFLQLNSVT TEDTATYYCA RLYYGFYGMD YWGQGTSVTV S

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Macromolecule #5: Light Chain of GluN1 Fab, 4F11

MacromoleculeName: Light Chain of GluN1 Fab, 4F11 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculoides (Temminck's mouse)
Molecular weightTheoretical: 13.916562 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MVSAIVLYVL LAAAAHSAFA MIVLTQSPAS LAVSLGQRAT ISCKASQSVD YDGNSYMNWY QQKPGQPPKL LIYAASNLES GIPARFSGS GSGTDFTLNI HPVEEEDAAT YYCQQGNEDP PTFGGGTKLE IK

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Macromolecule #6: Heavy Chain of GluN2A Fab, 28C

MacromoleculeName: Heavy Chain of GluN2A Fab, 28C / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculoides (Temminck's mouse)
Molecular weightTheoretical: 24.054979 KDa
SequenceString: QVTLKESGPG ILQPSQTLSL TCSFSGAAAA AAGVGVGWIR QPSGKGLEWL AHIAAAAAKR YNPALKSRLT ISKDTSSSQV FLKIASVAT ADTATYYCTR AAAAAAPYWG QGTLVTVSAK RADARTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE A KVQWKVDN ...String:
QVTLKESGPG ILQPSQTLSL TCSFSGAAAA AAGVGVGWIR QPSGKGLEWL AHIAAAAAKR YNPALKSRLT ISKDTSSSQV FLKIASVAT ADTATYYCTR AAAAAAPYWG QGTLVTVSAK RADARTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE A KVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNR

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Macromolecule #7: Light Chain of GluN2A Fab, 28C

MacromoleculeName: Light Chain of GluN2A Fab, 28C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculoides (Temminck's mouse)
Molecular weightTheoretical: 22.412863 KDa
SequenceString: DIQMTQSPAS LSVSVGETVT ITCRAAAAAA AALAWYQQKQ GKSPQLLVAA AAAAADGVPS RFSGSGSGTQ YSLKINSLQS EDFGSYYCQ AAAAAPWTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPAS LSVSVGETVT ITCRAAAAAA AALAWYQQKQ GKSPQLLVAA AAAAADGVPS RFSGSGSGTQ YSLKINSLQS EDFGSYYCQ AAAAAPWTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRG

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Macromolecule #8: Heavy Chain of GluN2B Fab2

MacromoleculeName: Heavy Chain of GluN2B Fab2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculoides (Temminck's mouse)
Molecular weightTheoretical: 26.659951 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVSAIVLYVL LAAAAHSAFA DVKLQESGGG LVQPGGSLKL SCAASGFTFS SYTMSWVRQT PEKRLEWVAY ISNGGGGTYY PDTVKGRFT ISRDNAKNTL YLQMNSLKED TAMYYCARPS RGGSSYWYFD VWGAGTTVTV SSAKTKGPSV FPLAPSSKST S GGTAALGC ...String:
MVSAIVLYVL LAAAAHSAFA DVKLQESGGG LVQPGGSLKL SCAASGFTFS SYTMSWVRQT PEKRLEWVAY ISNGGGGTYY PDTVKGRFT ISRDNAKNTL YLQMNSLKED TAMYYCARPS RGGSSYWYFD VWGAGTTVTV SSAKTKGPSV FPLAPSSKST S GGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR HH HHHHHHH H

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Macromolecule #9: Light Chain of GluN2B Fab2

MacromoleculeName: Light Chain of GluN2B Fab2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculoides (Temminck's mouse)
Molecular weightTheoretical: 28.581771 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVSAIVLYVL LAAAAHSAFA DIQMTQSPSS LSASLGGKVT ITCKASQDIN KYIAWYQHKP GKGPRLLIHY TSSLQPGIPS RFSGSGSGR DYSFSISNLE PEDIATYYCL QYDNLYTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String:
MVSAIVLYVL LAAAAHSAFA DIQMTQSPSS LSASLGGKVT ITCKASQDIN KYIAWYQHKP GKGPRLLIHY TSSLQPGIPS RFSGSGSGR DYSFSISNLE PEDIATYYCL QYDNLYTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGECGSGSW SH PQFEKGG GSGGGSGGSA WSHPQFEK

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 20 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #13: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid

MacromoleculeName: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid
type: ligand / ID: 13 / Number of copies: 2 / Formula: 7RC
Molecular weightTheoretical: 252.205 Da
Chemical component information

ChemComp-7RC:
(2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45676
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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