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- EMDB-72078: Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (cla... -

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Basic information

Entry
Database: EMDB / ID: EMD-72078
TitleNative GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate bound state
Map data
Sample
  • Complex: Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate-bound state
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2A
    • Protein or peptide: Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
    • Protein or peptide: Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsligand-gated ion channel / NMDA / antibody / native / TRANSPORT PROTEIN
Function / homology
Function and homology information


Assembly and cell surface presentation of NMDA receptors / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / sensory organ development / directional locomotion / pons maturation / regulation of cell communication / olfactory learning ...Assembly and cell surface presentation of NMDA receptors / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / sensory organ development / directional locomotion / pons maturation / regulation of cell communication / olfactory learning / conditioned taste aversion / regulation of respiratory gaseous exchange / fear response / protein localization to postsynaptic membrane / serotonin metabolic process / suckling behavior / propylene metabolic process / sleep / locomotion / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / neurotransmitter receptor complex / ligand-gated sodium channel activity / response to morphine / glutamate receptor signaling pathway / regulation of axonogenesis / neuromuscular process / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / transport vesicle membrane / protein heterotetramerization / male mating behavior / regulation of synapse assembly / regulation of cAMP/PKA signal transduction / glycine binding / startle response / dopamine metabolic process / monoatomic cation transmembrane transport / behavioral response to pain / regulation of postsynaptic membrane potential / associative learning / social behavior / regulation of neuronal synaptic plasticity / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / monoatomic cation channel activity / calcium ion homeostasis / regulation of neuron apoptotic process / glutamate-gated calcium ion channel activity / neurogenesis / sensory perception of pain / ionotropic glutamate receptor signaling pathway / sodium ion transmembrane transport / synaptic membrane / cytoplasmic vesicle membrane / response to amphetamine / adult locomotory behavior / learning / regulation of membrane potential / synaptic transmission, glutamatergic / excitatory postsynaptic potential / locomotory behavior / protein catabolic process / regulation of long-term neuronal synaptic plasticity / neuron cellular homeostasis / postsynaptic density membrane / cerebral cortex development / regulation of synaptic plasticity / negative regulation of protein catabolic process / visual learning / modulation of chemical synaptic transmission / calcium ion transmembrane transport / response to wounding / calcium channel activity / memory / long-term synaptic potentiation / intracellular calcium ion homeostasis / synaptic vesicle / synaptic vesicle membrane / calcium ion transport / late endosome / growth cone / presynaptic membrane / response to ethanol / dendritic spine / chemical synaptic transmission / in utero embryonic development / negative regulation of neuron apoptotic process / postsynaptic membrane / transcription by RNA polymerase II / learning or memory / cytoskeleton
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 2A / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKim J / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To Be Published
Title: Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate-bound state
Authors: Kim J / Gouaux E
History
DepositionAug 11, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72078.png

Downloads & links

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Map

FileDownload / File: emd_72078.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 336 pix.
= 468.384 Å		1.39 Å/pix.
x 336 pix.
= 468.384 Å		1.39 Å/pix.
x 336 pix.
= 468.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.394 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.05210936 - 0.120830834
Average (Standard dev.)0.00015940022 (±0.0034759063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 468.38403 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpen map

Fileemd_72078_additional_1.map
AnnotationSharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72078_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72078_half_map_2.map
Projections & Slices
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Sample components

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Entire : Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (cla...

EntireName: Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate-bound state
Components
  • Complex: Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate-bound state
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2A
    • Protein or peptide: Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
    • Protein or peptide: Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (cla...

SupramoleculeName: Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 667 KDa

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Macromolecule #1: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 166.162062 KDa
SequenceString: MKPSAECCSP KFWLVLAVLA VSGSKARSQK SAPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPKS IITRICDLM SDRKIQGVVL ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS IEQQASVMLN I MEEYDWYI ...String:
MKPSAECCSP KFWLVLAVLA VSGSKARSQK SAPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPKS IITRICDLM SDRKIQGVVL 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 SHLKHGTGDK HGVVGGVPAP WEKN LTNVD WEDRSGGNFC RSCPSKLHNY SSTVAGQNSG RQACIRCEAC KKAGNLYDIS EDNSLQELDQ PAAPVAVSSN ASTTK YPQS PTNSKAQKKN RNKLRRQHSY DTFVDLQKEE AALAPRSVSL KDKGRFMDGS PYAHMFEMPA GESSFANKSS VTTAGH HHN NPGSGYMLSK SLYPDRVTQN PFIPTFGDDQ CLLHGSKSYF FRQPTVAGAS KTRPDFRALV TNKPVVSALH GAVPGRF QK DICIGNQSNP CVPNNKNPRA FNGSSNGHVY EKLSSIESDV

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 105.61782 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 MEARDLEARV 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 YGFCVDLLIK 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 #3: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11

MacromoleculeName: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.432527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA QGQMQQSGAE LVKPGASVKL SCKTSGFSFS TSYINWLKQK PGQSLEWIAW IYAGTDGTSY NQKFTDKAQ LTVDTSSSTA YMQFSSLTTD DSAIYYCARE GIYYGNYAGF TYWGQGTLVT VSAAKTTPPS VYPLAPGSAA Q TNSMVTLG ...String:
MVSAIVLYVL LAAAAHSAFA QGQMQQSGAE LVKPGASVKL SCKTSGFSFS TSYINWLKQK PGQSLEWIAW IYAGTDGTSY NQKFTDKAQ LTVDTSSSTA YMQFSSLTTD DSAIYYCARE GIYYGNYAGF TYWGQGTLVT VSAAKTTPPS VYPLAPGSAA Q TNSMVTLG CLVKGYFPEP VTVTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK LV PRGSAAA AGTGSGGGDY KDHDGDYKDH DIDYKDDDDK

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Macromolecule #4: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11

MacromoleculeName: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.909961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA DIVMTQSPSS LAVTAGEKVT MRCKSSQSLL WSVNQNNYLS WYQQKQGQPP KLLIYGASIR ESWVPDRFT GSGSGTDFTL TISNVHAEDL AVYYCQHNHG SFLPYTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS V VCFLNNFY ...String:
MVSAIVLYVL LAAAAHSAFA DIVMTQSPSS LAVTAGEKVT MRCKSSQSLL WSVNQNNYLS WYQQKQGQPP KLLIYGASIR ESWVPDRFT GSGSGTDFTL TISNVHAEDL AVYYCQHNHG SFLPYTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS V VCFLNNFY PKDINVKWKI DGSERQNGVL NSWTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RN ECSN

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Macromolecule #5: Glutamate receptor ionotropic, NMDA 2A

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 165.619891 KDa
SequenceString: MGRLGYWTLL VLPALLVWHG PAQNAAAEKG TPALNIAVLL GHSHDVTERE LRNLWGPEQA TGLPLDVNVV ALLMNRTDPK SLITHVCDL MSGARIHGLV FGDDTDQEAV AQMLDFISSQ TFIPILGIHG GASMIMADKD PTSTFFQFGA SIQQQATVML K IMQDYDWH ...String:
MGRLGYWTLL VLPALLVWHG PAQNAAAEKG TPALNIAVLL 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 YGQTEK 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 QYMTKFNQRG VEDALVSL K TGKLDAFIYD AAVLNYKAGR DEGCKLVTIG SGYIFATTGY GIALQKGSPW KRQIDLALLQ FVGDGEMEEL ETLWLTGIC HNEKNEVMSS QLDIDNMAGV FYMLAAAMAL SLITFIWEHL FYWKLRFCFT GVCSDRPGLL FSISRGIYSC IHGVHIEEKK KSPDFNLTG SQSNMLKLLR SAKNISNMSN MNSSRMDSPK RAADFIQRGS LIVDMVSDKG NLIYSDNRSF QGKDSIFGEN M NELQTFVA NRHKDSLSNY VFQGQHPLTL NESNPNTVEV AVSTESKGNS RPRQLWKKSM ESLRQDSLNQ NPVSQRDEKT AE NRTHSLK SPRYLPEEVA HSDISETSSR ATCHREPDNN KNHKTKDNFK RSMASKYPKD CSEVERTYVK TKASSPRDKI YTI DGEKEP SFHLDPPQFI ENIVLPENVD FPDTYQDHNE NFRKGDSTLP MNRNPLHNED GLPNNDQYKL YAKHFTLKDK GSPH SEGSD RYRQNSTHCR SCLSNLPTYS GHFTMRSPFK CDACLRMGNL YDIDEDQMLQ ETGNPATREE AYQQDWSQNN ALQFQ KNKL KINRQHSYDN ILDKPREIDL SRPSRSISLK DRERLLEGNL YGSLFSVPSS KLLGNKSSLF PQGLEDSKRS KSLLPD HTS DNPFLHTYGD DQRLVIGRCP SDPYKHSLPS QAVNDSYLRS SLRSTASYCS RDSRGHSDVY ISEHVMPYAA NKNNMYS TP RVLNSCSNRR VYKKMPSIES DV

UniProtKB: Glutamate receptor ionotropic, NMDA 2A

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Macromolecule #6: Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2

MacromoleculeName: Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.448522 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVSAIVLYVL LAAAAHSAFA QVQLQQSGAE LMKPGASVKI SCKATGYTFR SYWIEWLKQR PGHGLEWIGE ILPGSGRTNY NEKFKGKAT ITADTSSNTA YMQLSSLTSE DSAVYYCTRS RGTMITREFT YWGQGALVTV SA

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Macromolecule #7: Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2

MacromoleculeName: Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.989831 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVSAIVLYVL LAAAAHSAFA DIVLTQSPAS LAVSLGQRAT ISCRASESVE YYGTTLMQWY QQKPGQPPKL LIYAASNVDS GVPARFSGS GSGTDFSLNI HPVEEDDIAM YFCQQSRKVP STFGGGTKLE IK

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration0.05 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 290 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9851 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model from 2D class average
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 296585
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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