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- EMDB-61251: Native GluA1/GluA4 ATD dimer binding with 1D8 and 11B8 -

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Basic information

Entry
Database: EMDB / ID: EMD-61251
TitleNative GluA1/GluA4 ATD dimer binding with 1D8 and 11B8
Map data
Sample
  • Complex: Native GluA1/GluA4 ATD dimer binding with 1D8 and 11B8
    • Protein or peptide: Glutamate receptor
    • Protein or peptide: Glutamate receptor
    • Protein or peptide: 1D8 Fab
    • Protein or peptide: 11B8 scFV
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAMPA receptor / native / GluA1 / GluA4 / ATD 1D8 / 11B8 / MEMBRANE PROTEIN / AMPAR
Function / homology
Function and homology information


COPII-mediated vesicle transport / Cargo concentration in the ER / Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / axonal spine / cellular response to ammonium ion / dendritic spine membrane / long-term synaptic depression ...COPII-mediated vesicle transport / Cargo concentration in the ER / Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / axonal spine / cellular response to ammonium ion / dendritic spine membrane / long-term synaptic depression / perisynaptic space / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / long-term memory / synapse assembly / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / receptor internalization / recycling endosome / postsynaptic density membrane / modulation of chemical synaptic transmission / synaptic vesicle membrane / dendritic spine / neuronal cell body / glutamatergic synapse / cell surface / endoplasmic reticulum / plasma membrane
Similarity search - Function
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 / Glutamate receptor
Similarity search - Component
Biological speciesSus scrofa (pig) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsLi X / Li R / Wei Y / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92157102 China
CitationJournal: To Be Published
Title: Native GluA1/GluA4 ATD dimer binding with 1D8 and 11B8
Authors: Li X / Li R / Wei Y / Zhao Y
History
DepositionAug 22, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61251.png

Downloads & links

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Map

FileDownload / File: emd_61251.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-1.2900289 - 1.7312684
Average (Standard dev.)-0.0015277439 (±0.022884062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61251_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61251_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native GluA1/GluA4 ATD dimer binding with 1D8 and 11B8

EntireName: Native GluA1/GluA4 ATD dimer binding with 1D8 and 11B8
Components
  • Complex: Native GluA1/GluA4 ATD dimer binding with 1D8 and 11B8
    • Protein or peptide: Glutamate receptor
    • Protein or peptide: Glutamate receptor
    • Protein or peptide: 1D8 Fab
    • Protein or peptide: 11B8 scFV
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Native GluA1/GluA4 ATD dimer binding with 1D8 and 11B8

SupramoleculeName: Native GluA1/GluA4 ATD dimer binding with 1D8 and 11B8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Glutamate receptor

MacromoleculeName: Glutamate receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 99.389758 KDa
SequenceString: MRIICRQIVL LFSGFWGLAM GAFPSSVQIG GLFIRNTDQE YTAFRLAIFL HNTSPNASEA PFNLVPHVDN IETANSFAVT NAFCSQYSR GVFAIFGLYD KRSVHTLTSF CSALHISLIT PSFPTEGESQ FVLQLRPSLR GALLSLLDHY EWNCFVFLYD T DRGYSILQ ...String:
MRIICRQIVL LFSGFWGLAM GAFPSSVQIG GLFIRNTDQE YTAFRLAIFL HNTSPNASEA PFNLVPHVDN IETANSFAVT NAFCSQYSR GVFAIFGLYD KRSVHTLTSF CSALHISLIT PSFPTEGESQ FVLQLRPSLR GALLSLLDHY EWNCFVFLYD T DRGYSILQ AIMEKAGQNG WHVSAICVEN FNDVSYRQLL EELDRRQEKK FVIDCEIERL QNILEQIVSV GKHVKGYHYI IA NLGFKDI SLERFIHGGA NVTGFQLVDF NTPMVTKLMD RWKKLDQREY PGSETPPKYT SALTYDGVLV MAETFRNLRR QKI DISRRG NAGDCLANPA APWGQGIDME RTLKQVQIQG LTGNVQFDHY GRRVNYTMDV FELKSTGPRK VGYWNDMDKL VLIQ DVPTL GNDTAAIENR TVVVTTIMES PYVMYKKNHE MFEGNDKYEG YCVDLASEIA KHIGIKYKIA IVPDGKYGAR DADTK IWNG MVGELVYGKA EIAIAPLTIT LVREEVIDFS KPFMSLGISI MIKKPQKSKP GVFSFLDPLA YEIWMCIVFA YIGVSV VLF LVSRFSPYEW HTEEPEDGKE GPSDQPPNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTA NL AAFLTVERMV SPIESAEDLA KQTEIAYGTL DSGSTKEFFR RSKIAVYEKM WTYMRSAEPS VFTRTTAEGV ARVRKSKG K FAFLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGVATPKG SSLRTPVNLA VLKLSEAGVL DKLKNKWWYD KGECGPKDS GSKDKTSALS LSNVAGVFYI LVGGLGLAML VALIEFCYKS RAEAKRMKVA KSAQTFNPTS SQNTQNLATY REGYNVYGTE SIKI

UniProtKB: Glutamate receptor

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Macromolecule #2: Glutamate receptor

MacromoleculeName: Glutamate receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 101.565953 KDa
SequenceString: MQHIFAFFCT GFLGAVVGAN FPNNIQIGGL FPNQQSQEHA AFRFALSQLT EPPKLLPQID IVNISDSFEM TYRFCSQFSK GVYAIFGFY ERRTVNMLTS FCGALHVCFI TPSFPVDTSN QFVLQLRPEL QDALISIIDH YKWQKFVYIY DADRGLSVLQ K VLDTAAEK ...String:
MQHIFAFFCT GFLGAVVGAN FPNNIQIGGL FPNQQSQEHA AFRFALSQLT EPPKLLPQID IVNISDSFEM TYRFCSQFSK GVYAIFGFY ERRTVNMLTS FCGALHVCFI TPSFPVDTSN QFVLQLRPEL QDALISIIDH YKWQKFVYIY DADRGLSVLQ K VLDTAAEK NWQVTAVNIL TTTEEGYRML FQDLEKKKER LVVVDCESER LNAILGQIIK LEKNGIGYHY ILANLGFMDI DL NKFKESG ANVTGFQLVN YTDTIPAKIM QQWKTSDARD HTRVDWKRPK YTSALTYDGV KVMAEAFQSL RRQRIDISRR GNA GDCLAN PAVPWGQGID IQRALQQVRF EGLTGNVQFN EKGRRTNYTL HVIEMKHDGI RKIGYWNEDD KFVPAATDAQ AGGD NSSVQ NRTYIVTTIL EDPYVMLKKN ANQFEGNDRY EGYCVELAAE IAKHVGYSYR LEIVSDGKYG ARDPDTKAWN GMVGE LVYG RADVAVAPLT ITLVREEVID FSKPFMSLGI SIMIKKPQKS KPGVFSFLDP LAYEIWMCIV FAYIGVSVVL FLVSRF SPY EWHSEEFEEG RDQTTSDQSN EFGIFNSLWF SLGAFMQQGC DISPRSLSGR IVGGVWWFFT LIIISSYTAN LAAFLTV ER MVSPIESAED LAKQTEIAYG TLEAGSTKEF FRRSKIAVFE KMWTYMKSAE PSVFVRTTEE GMIRVRKSKG KYAYLLES T MNEYIEQRKP CDTMKVGGNL DSKGYGIATP KGSALRGPVN LAVLKLSEQG VLDKLKSKWW YDKGECGSKD SGSKDKTSA LSLSNVAGVF YILIGGLGLA MLVALIEFCY KSRSESKRMK GFCLIPQQSI NEAIRTSTLP RNSGAGASGG GSGENGRVVS HDFPKSMQS IPCMSHSTGM PLGATGL

UniProtKB: Glutamate receptor

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Macromolecule #3: 1D8 Fab

MacromoleculeName: 1D8 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 18.570826 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #4: 11B8 scFV

MacromoleculeName: 11B8 scFV / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.244289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVKLLESGGG LVQPGGSLKL SCAASGFDFS EYWMSWVRQA PGKGLEWIGE INPDSSSIDY TPSLKDKIII SRDNAKKTLY LQLSKVRSE DTALYYCARP RGNYVVMDYW GQGTSVTVSS GGSGGSGGSG GSGGSNIVLT QSPASLAVSL GQRATISCRA S ESVDSYGS ...String:
EVKLLESGGG LVQPGGSLKL SCAASGFDFS EYWMSWVRQA PGKGLEWIGE INPDSSSIDY TPSLKDKIII SRDNAKKTLY LQLSKVRSE DTALYYCARP RGNYVVMDYW GQGTSVTVSS GGSGGSGGSG GSGGSNIVLT QSPASLAVSL GQRATISCRA S ESVDSYGS SFVHWYQQKP GQPPKLLIFL ASKLESGVPA RFSGSGSRTD FTLTIDPVEA DDAATYYCQQ TNEDPYTFGG GT KLEIKRA WSHPQFEKGG GSGGGSGGSN WSHPQFEK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k 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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138139
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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