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- EMDB-9389: Architecture and subunit arrangement of native AMPA receptors -

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Basic information

Entry
Database: EMDB / ID: EMD-9389
TitleArchitecture and subunit arrangement of native AMPA receptors
Map dataComplex
Sample
  • Complex: Native GluA1/GluA2/GluA3/GluA2 complex bound with MPQX
    • Complex: ATD-LBD layers of native tri-heteromeric A1A2A3A2 AMPAR
      • Protein or peptide: x 9 types
    • Complex: LBD-TMD layers of native tri-heteromeric A1A2A3A2 AMPAR
    • Complex: ATD layer of native tri-heteromeric A1A2A3A2 AMPAR
  • Ligand: x 2 types
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / COPII-mediated vesicle transport / positive regulation of membrane potential / chemical synaptic transmission, postsynaptic / cellular response to ammonium ion ...Presynaptic depolarization and calcium channel opening / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / COPII-mediated vesicle transport / positive regulation of membrane potential / chemical synaptic transmission, postsynaptic / cellular response to ammonium ion / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / LGI-ADAM interactions / neuron spine / myosin V binding / Trafficking of AMPA receptors / regulation of AMPA receptor activity / neurotransmitter receptor internalization / channel regulator activity / membrane hyperpolarization / dendritic spine membrane / postsynaptic neurotransmitter receptor diffusion trapping / response to arsenic-containing substance / cellular response to dsRNA / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / parallel fiber to Purkinje cell synapse / neurotransmitter receptor localization to postsynaptic specialization membrane / long-term synaptic depression / beta-2 adrenergic receptor binding / protein kinase A binding / cellular response to peptide hormone stimulus / neuronal cell body membrane / neuromuscular junction development / spine synapse / spinal cord development / dendritic spine neck / voltage-gated calcium channel complex / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / transmission of nerve impulse / AMPA glutamate receptor activity / regulation of postsynaptic membrane neurotransmitter receptor levels / Trafficking of GluR2-containing AMPA receptors / membrane depolarization / immunoglobulin binding / calcium channel regulator activity / AMPA glutamate receptor complex / neuronal action potential / kainate selective glutamate receptor activity / excitatory synapse / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / adenylate cyclase binding / cellular response to organic cyclic compound / asymmetric synapse / G-protein alpha-subunit binding / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / voltage-gated calcium channel activity / regulation of postsynaptic membrane potential / long-term memory / glutamate receptor binding / synaptic cleft / positive regulation of synaptic transmission / response to electrical stimulus / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / hippocampal mossy fiber to CA3 synapse / cytoskeletal protein binding / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / monoatomic ion transmembrane transport / positive regulation of synaptic transmission, glutamatergic / SNARE binding / response to cocaine / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / cellular response to amino acid stimulus / protein tetramerization / regulation of synaptic plasticity / modulation of chemical synaptic transmission
Similarity search - Function
Voltage-dependent calcium channel, gamma-2 subunit / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel ...Voltage-dependent calcium channel, gamma-2 subunit / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 1 / Glutamate receptor 2 / Glutamate receptor 3 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Rat (rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsGouaux E / Zhao Y
CitationJournal: Science / Year: 2019
Title: Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM.
Authors: Yan Zhao / Shanshuang Chen / Adam C Swensen / Wei-Jun Qian / Eric Gouaux /
Abstract: Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric ...Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo-electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating.
History
DepositionJan 3, 2019-
Header (metadata) releaseApr 24, 2019-
Map releaseApr 24, 2019-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6njn
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9389.png

Downloads & links

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Map

FileDownload / File: emd_9389.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 320 pix.
= 550.4 Å		1.72 Å/pix.
x 320 pix.
= 550.4 Å		1.72 Å/pix.
x 320 pix.
= 550.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.044 / Movie #1: 0.044
Minimum - Maximum-0.0767264 - 0.23889424
Average (Standard dev.)0.00044798778 (±0.004797919)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 550.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z550.400550.400550.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0770.2390.000

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Supplemental data

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Additional map: Complex

Fileemd_9389_additional_1.map
AnnotationComplex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Complex

Fileemd_9389_additional_2.map
AnnotationComplex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Complex

Fileemd_9389_additional_3.map
AnnotationComplex
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/GluA2/GluA3/GluA2 complex bound with MPQX

EntireName: Native GluA1/GluA2/GluA3/GluA2 complex bound with MPQX
Components
  • Complex: Native GluA1/GluA2/GluA3/GluA2 complex bound with MPQX
    • Complex: ATD-LBD layers of native tri-heteromeric A1A2A3A2 AMPAR
      • Protein or peptide: Glutamate receptor 1
      • Protein or peptide: Glutamate receptor 2GRIA2
      • Protein or peptide: Glutamate receptor 3
      • Protein or peptide: A'-C' auxiliary proteins
      • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
      • Protein or peptide: 11B8 scFv
      • Protein or peptide: 15F1 Fab light chain
      • Protein or peptide: 15F1 Fab heavy chain
      • Protein or peptide: 5B2 Fab
    • Complex: LBD-TMD layers of native tri-heteromeric A1A2A3A2 AMPAR
    • Complex: ATD layer of native tri-heteromeric A1A2A3A2 AMPAR
  • Ligand: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Native GluA1/GluA2/GluA3/GluA2 complex bound with MPQX

SupramoleculeName: Native GluA1/GluA2/GluA3/GluA2 complex bound with MPQX
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #2: ATD-LBD layers of native tri-heteromeric A1A2A3A2 AMPAR

SupramoleculeName: ATD-LBD layers of native tri-heteromeric A1A2A3A2 AMPAR
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#9
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: LBD-TMD layers of native tri-heteromeric A1A2A3A2 AMPAR

SupramoleculeName: LBD-TMD layers of native tri-heteromeric A1A2A3A2 AMPAR
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #4: ATD layer of native tri-heteromeric A1A2A3A2 AMPAR

SupramoleculeName: ATD layer of native tri-heteromeric A1A2A3A2 AMPAR / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1-#3, #6-#9
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Glutamate receptor 1

MacromoleculeName: Glutamate receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rat (rat)
Molecular weightTheoretical: 101.518773 KDa
SequenceString: MPYIFAFFCT GFLGAVVGAN FPNNIQIGGL FPNQQSQEHA AFRFALSQLT EPPKLLPQID IVNISDSFEM TYRFCSQFSK GVYAIFGFY ERRTVNMLTS FCGALHVCFI TPSFPVDTSN QFVLQLRPEL QEALISIIDH YKWQTFVYIY DADRGLSVLQ R VLDTAAEK ...String:
MPYIFAFFCT GFLGAVVGAN FPNNIQIGGL FPNQQSQEHA AFRFALSQLT EPPKLLPQID IVNISDSFEM TYRFCSQFSK GVYAIFGFY ERRTVNMLTS FCGALHVCFI TPSFPVDTSN QFVLQLRPEL QEALISIIDH YKWQTFVYIY DADRGLSVLQ R VLDTAAEK NWQVTAVNIL TTTEEGYRML FQDLEKKKER LVVVDCESER LNAILGQIVK LEKNGIGYHY ILANLGFMDI DL NKFKESG ANVTGFQLVN YTDTIPARIM QQWRTSDSRD 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 KGSALGAPVN LAVLKLAEQG ALDKLKAKWW YDKGECGSKD SGSKDKTSA LSLSNVAGVF YILIGGLGLA MLVALIEFCY KSRSESKRMK GFCLIPQQSI NEAIRTSTLP RNSGAGASGG GGSGENGRVV SQDFPKSMQ SIPCMSHSSG MPLGATGL

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Macromolecule #2: Glutamate receptor 2

MacromoleculeName: Glutamate receptor 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rat (rat)
Molecular weightTheoretical: 98.783805 KDa
SequenceString: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA ...String:
MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA AEKKWQVTAI NVGNINNDKK DETYRSLFQD LELKKERRVI LDCERDKVND IVDQVITIGK HVKGYHYIIA NL GFTDGDL LKIQFGGANV SGFQIVDYDD SLVSKFIERW STLEEKEYPG AHTATIKYTS ALTYDAVQVM TEAFRNLRKQ RIE ISRRGN AGDCLANPAV PWGQGVEIER ALKQVQVEGL SGNIKFDQNG KRINYTINIM ELKTNGPRKI GYWSEVDKMV VTLT ELPSG NDTSGLENKT VVVTTILESP YVMMKKNHEM LEGNERYEGY CVDLAAEIAK HCGFKYKLTI VGDGKYGARD ADTKI WNGM VGELVYGKAD IAIAPLTITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVV LFL VSRFSPYEWH TEEFEDGRET QSSESTNEFG IFNSLWFSLG AFMRQGCDIS PRSLSGRIVG GVWWFFTLII ISSYTAN LA AFLTVERMVS PIESAEDLSK QTEIAYGTLD SGSTKEFFRR SKIAVFDKMW TYMRSAEPSV FVRTTAEGVA RVRKSKGK Y AYLLESTMNE YIEQRKPCDT MKVGGNLDSK GYGIATPKGS SLGAAVNLAV LKLAEQGALD KLKNKWWYDK GECGAKDSG SKEKTSALSL SNVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK NPQNINPSSS QNSQNFATYK EGYNVYGIES VKI

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Macromolecule #3: Glutamate receptor 3

MacromoleculeName: Glutamate receptor 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rat (rat)
Molecular weightTheoretical: 100.55668 KDa
SequenceString: MGQSVLRAVF FLVLGLLGHS HGGFPNTISI GGLFMRNTVQ EHSAFRFAVQ LYNTNQNTTE KPFHLNYHVD HLDSSNSFSV TNAFCSQFS RGVYAIFGFY DQMSMNTLTS FCGALHTSFV TPSFPTDADV QFVIQMRPAL KGAILSLLSY YKWEKFVYLY D TERGFSVL ...String:
MGQSVLRAVF FLVLGLLGHS HGGFPNTISI GGLFMRNTVQ EHSAFRFAVQ LYNTNQNTTE KPFHLNYHVD HLDSSNSFSV TNAFCSQFS RGVYAIFGFY DQMSMNTLTS FCGALHTSFV TPSFPTDADV QFVIQMRPAL KGAILSLLSY YKWEKFVYLY D TERGFSVL QAIMEAAVQN NWQVTARSVG NIKDVQEFRR IIEEMDRRQE KRYLIDCEVE RINTILEQVV ILGKHSRGYH YM LANLGFT DILLERVMHG GANITGFQIV NNENPMVQQF IQRWVRLDER EFPEAKNAPL KYTSALTHDA ILVIAEAFRY LRR QRVDVS RRGSAGDCLA NPAVPWSQGI DIERALKMVQ VQGMTGNIQF DTYGRRTNYT IDVYEMKVSG SRKAGYWNEY ERFV PFSDQ QISNDSSSSE NRTIVVTTIL ESPYVMYKKN HEQLEGNERY EGYCVDLAYE IAKHVRIKYK LSIVGDGKYG ARDPE TKIW NGMVGELVYG RADIAVAPLT ITLVREEVID FSKPFMSLGI SIMIKKPQKS KPGVFSFLDP LAYEIWMCIV FAYIGV SVV LFLVSRFSPY EWHLEDNNEE PRDPQSPPDP PNEFGIFNSL WFSLGAFMQQ GCDISPRSLS GRIVGGVWWF FTLIIIS SY TANLAAFLTV ERMVSPIESA EDLAKQTEIA YGTLDSGSTK EFFRRSKIAV YEKMWSYMKS AEPSVFTKTT ADGVARVR K SKGKFAFLLE STMNEYIEQR KPCDTMKVGG NLDSKGYGVA TPKGSALGTP VNLAVLKLSE QGILDKLKNK WWYDKGECG AKDSGSKDKT SALSLSNVAG VFYILVGGLG LAMMVALIEF CYKSRAESKR MKLTKNTQNF KPAPATNTQN YATYREGYNV YGTESVKI

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Macromolecule #4: A'-C' auxiliary proteins

MacromoleculeName: A'-C' auxiliary proteins / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rat (rat)
Molecular weightTheoretical: 13.039064 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)

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Macromolecule #5: Voltage-dependent calcium channel gamma-2 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-2 subunit / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rat (rat)
Molecular weightTheoretical: 35.938746 KDa
SequenceString: MGLFDRGVQM LLTTVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD ...String:
MGLFDRGVQM LLTTVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD SKKNSYSYGW SFYFGALSFI IAEMVGVLAV HMFIDRHKQL RATARATDYL QASAITRIPS YRYRYQRRSR SS SRSTEPS HSRDASPVGV KGFNTLPSTE ISMYTLSRDP LKAATTPTAT YNSDRDNSFL QVHNCIQKDS KDSLHANTAN RRT TPV

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Macromolecule #6: 11B8 scFv

MacromoleculeName: 11B8 scFv / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.511527 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVKLLESGGG LVQPGGSLKL SCAASGFDFS EYWMSWVRQA PGKGLEWIGE INPDSSSIDY TPSLKDKIII SRDNAKKTLY LQLSKVRSE DTALYYCARP RGNYVVMDYW GQGTSVTVSS SGGGGSGGGG SGGGGNIVLT QSPASLAVSL GQRATISCRA S ESVDSYGS ...String:
EVKLLESGGG LVQPGGSLKL SCAASGFDFS EYWMSWVRQA PGKGLEWIGE INPDSSSIDY TPSLKDKIII SRDNAKKTLY LQLSKVRSE DTALYYCARP RGNYVVMDYW GQGTSVTVSS SGGGGSGGGG SGGGGNIVLT QSPASLAVSL GQRATISCRA S ESVDSYGS SFVHWYQQKP GQPPKLLIFL ASKLESGVPA RFSGSGSRTD FTLTIDPVEA DDAATYYCQQ TNEDPYTFGG GT KLEIKRA SNWSHPQFEK

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Macromolecule #7: 15F1 Fab light chain

MacromoleculeName: 15F1 Fab light chain / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.11166 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEIQMTQTTS SLSASLGDRV TISCRASQDI SNYLSWYQQK PDGTVKLLIY YTSRLHSGVP SRFSGSGSGI DYSLTINNLE QEDFATYFC QQGNTLPLTF GAGTKLELKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD ...String:
MEIQMTQTTS SLSASLGDRV TISCRASQDI SNYLSWYQQK PDGTVKLLIY YTSRLHSGVP SRFSGSGSGI DYSLTINNLE QEDFATYFC QQGNTLPLTF GAGTKLELKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNECSNW SHPQFEK

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Macromolecule #8: 15F1 Fab heavy chain

MacromoleculeName: 15F1 Fab heavy chain / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.975439 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA MQAQLKESGP GLVAPSQSLS ITCTVSGFSL TNYGVHWVRQ PPGKGLEWLG VIWAGGSTNY NSALMSRVS ISKDNSKSQV FLKMNSLQTD DTVMYYCARE DYDYDWHFDV WGAGTTVTVS SAKTTPPSVY PLAPGSAAQT N SMVTLGCL ...String:
MVSAIVLYVL LAAAAHSAFA MQAQLKESGP GLVAPSQSLS ITCTVSGFSL TNYGVHWVRQ PPGKGLEWLG VIWAGGSTNY NSALMSRVS ISKDNSKSQV FLKMNSLQTD DTVMYYCARE DYDYDWHFDV WGAGTTVTVS SAKTTPPSVY PLAPGSAAQT N SMVTLGCL VKGYFPEPVT VTWNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSSTWPSE TVTCNVAHPA SSTKVDKKLE VL FQGPGSG SADTITIRGY VRDNR

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Macromolecule #9: 5B2 Fab

MacromoleculeName: 5B2 Fab / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rat (rat)
Molecular weightTheoretical: 19.081451 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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #12: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquino...

MacromoleculeName: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
type: ligand / ID: 12 / Number of copies: 4 / Formula: ZK1
Molecular weightTheoretical: 409.254 Da
Chemical component information

ChemComp-ZK1:
{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / antagonist, medication*YM / Fanapanel

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMC4H11NO3Tris
0.1 % w/vdigitonindigitonin
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 10
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 161000

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6njn:
Architecture and subunit arrangement of native AMPA receptors

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