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- EMDB-16380: Resting state homomeric GluA1 AMPA receptor in complex with TARP ... -
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Open data
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Basic information
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Title | Resting state homomeric GluA1 AMPA receptor in complex with TARP gamma 3 | |||||||||
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![]() | AMPAR / ion channels / neurotransmission / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / neurotransmitter receptor transport, postsynaptic endosome to lysosome / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / LGI-ADAM interactions / myosin V binding ...Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / neurotransmitter receptor transport, postsynaptic endosome to lysosome / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / LGI-ADAM interactions / myosin V binding / Trafficking of AMPA receptors / regulation of AMPA receptor activity / neuron spine / neurotransmitter receptor internalization / channel regulator activity / response to arsenic-containing substance / cellular response to dsRNA / postsynaptic neurotransmitter receptor diffusion trapping / dendritic spine membrane / Synaptic adhesion-like molecules / glutamate-gated calcium ion channel activity / neurotransmitter receptor localization to postsynaptic specialization membrane / long-term synaptic depression / cellular response to peptide hormone stimulus / protein kinase A binding / neuronal cell body membrane / spinal cord development / Activation of AMPA receptors / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / adenylate cyclase binding / cellular response to organic cyclic compound / ionotropic glutamate receptor complex / excitatory synapse / asymmetric synapse / G-protein alpha-subunit binding / regulation of receptor recycling / neuronal action potential / voltage-gated calcium channel activity / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / protein targeting / glutamate receptor binding / positive regulation of synaptic transmission / long-term memory / response to electrical stimulus / presynaptic active zone membrane / glutamate-gated receptor activity / beta-2 adrenergic receptor binding / response to fungicide / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of synaptic transmission, glutamatergic / response to cocaine / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / long-term synaptic potentiation / cellular response to amino acid stimulus / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / modulation of chemical synaptic transmission / neuromuscular junction / protein localization / receptor internalization / response to organic cyclic compound / recycling endosome / response to toxic substance / cerebral cortex development / cellular response to growth factor stimulus / response to peptide hormone / synaptic vesicle membrane / small GTPase binding / recycling endosome membrane / G-protein beta-subunit binding / cell-cell junction / synaptic vesicle / presynapse / response to estradiol / presynaptic membrane / amyloid-beta binding / early endosome membrane / cell body / scaffold protein binding / postsynapse / chemical synaptic transmission / postsynaptic membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.82 Å | |||||||||
![]() | Zhang D / Ivica J / Krieger JM / Ho H / Yamashita K / Cais O / Greger I | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor. Authors: Danyang Zhang / Josip Ivica / James M Krieger / Hinze Ho / Keitaro Yamashita / Imogen Stockwell / Rozbeh Baradaran / Ondrej Cais / Ingo H Greger / ![]() ![]() Abstract: AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. ...AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. Despite their prominent expression throughout interneurons and glia, their role in long-term potentiation and their involvement in a range of neuropathologies, structural information for GluA2-lacking receptors is currently absent. Here we determine and characterize cryo-electron microscopy structures of the GluA1 homotetramer, fully occupied with TARPγ3 auxiliary subunits (GluA1/γ3). The gating core of both resting and open-state GluA1/γ3 closely resembles GluA2-containing receptors. However, the sequence-diverse N-terminal domains (NTDs) give rise to a highly mobile assembly, enabling domain swapping and subunit re-alignments in the ligand-binding domain tier that are pronounced in desensitized states. These transitions underlie the unique kinetic properties of GluA1. A GluA2 mutant (F231A) increasing NTD dynamics phenocopies this behaviour, and exhibits reduced synaptic responses, reflecting the anchoring function of the AMPAR NTD at the synapse. Together, this work underscores how the subunit-diverse NTDs determine subunit arrangement, gating properties and ultimately synaptic signalling efficiency among AMPAR subtypes. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.6 KB | Display | ![]() |
Images | ![]() | 86.2 KB | ||
Masks | ![]() | 45.2 MB | ![]() | |
Filedesc metadata | ![]() | 6.8 KB | ||
Others | ![]() ![]() | 42 MB 42 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 864.1 KB | Display | ![]() |
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Full document | ![]() | 863.7 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c1qMC ![]() 8c1pC ![]() 8c1rC ![]() 8c1sC ![]() 8c2hC ![]() 8c2iC ![]() 8p3qC ![]() 8p3sC ![]() 8p3tC ![]() 8p3uC ![]() 8p3vC ![]() 8p3wC ![]() 8p3xC ![]() 8p3yC ![]() 8p3zC ![]() 8pivC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
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-Half map: #1
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Sample components
-Entire : Homomeric GluA1 AMPA receptor in complex with TARP gamma 3
Entire | Name: Homomeric GluA1 AMPA receptor in complex with TARP gamma 3 |
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Components |
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-Supramolecule #1: Homomeric GluA1 AMPA receptor in complex with TARP gamma 3
Supramolecule | Name: Homomeric GluA1 AMPA receptor in complex with TARP gamma 3 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Glutamate receptor 1 flip isoform
Macromolecule | Name: Glutamate receptor 1 flip isoform / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 102.66193 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR ...String: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR VLDTAAEKNW QVTAVNILTT TEEGYRMLFQ DLEKKKERLV VVDCESERLN AILGQIVKLE KNGIGYHYIL AN LGFMDID LNKFKESGAN VTGFQLVNYT DTIPARIMQQ WRTSDSRDHT RVDWKRPKYT SALTYDGVKV MAEAFQSLRR QRI DISRRG NAGDCLANPA VPWGQGIDIQ RALQQVRFEG LTGNVQFNEK GRRTNYTLHV IEMKHDGIRK IGYWNEDDKF VPAA TDAQA GGDNSSVQNR TYIVTTILED PYVMLKKNAN QFEGNDRYEG YCVELAAEIA KHVGYSYRLE IVSDGKYGAR DPDTK AWNG MVGELVYGRA DVAVAPLTIT LVREEVIDFS KPFMSLGISI MIKKPQKSKP GVFSFLDPLA YEIWMCIVFA YIGVSV VLF LVSRFSPYEW HSEEFEEGRD QTTSDQSNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTA NL AAFLTVERMV SPIESAEDLA KQTEIAYGTL EAGSTKEFFR RSKIAVFEKM WTYMKSAEPS VFVRTTEEGM IRVRKSKG K YAYLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGIATPKG SALRGPVNLA VLKLSEQGVL DKLKSKWWYD KGECGSKDS GSKDKTSALS LSNVAGVFYI LIGGLGLAML VALIEFCYKS RSESKRMKGF CLIPQQSINE AIRTSTLPRN SGAGASGGGG SGENGRVVS QDFPKSMQSI PCMSHSSGMP LGATGL UniProtKB: Glutamate receptor 1 |
-Macromolecule #2: Voltage-dependent calcium channel gamma-3 subunit
Macromolecule | Name: Voltage-dependent calcium channel gamma-3 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 35.435332 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: RMCDRGIQML ITTVGAFAAF SLMTIAVGTD YWLYSRGVCR TKSTSDNETS RKNEEVMTHS GLWRTCCLEG AFRGVCKKID HFPEDADYE QDTAEYLLRA VRASSVFPIL SVTLLFFGGL CVAASEFHRS RHSVILSAGI FFVSAGLSNI IGIIVYISAN A GDPGQRDS ...String: RMCDRGIQML ITTVGAFAAF SLMTIAVGTD YWLYSRGVCR TKSTSDNETS RKNEEVMTHS GLWRTCCLEG AFRGVCKKID HFPEDADYE QDTAEYLLRA VRASSVFPIL SVTLLFFGGL CVAASEFHRS RHSVILSAGI FFVSAGLSNI IGIIVYISAN A GDPGQRDS KKSYSYGWSF YFGAFSFIIA EIVGVVAVHI YIEKHQQLRA RSHSELLKKS TFARLPPYRY RFRRRSSSRS TE PRSRDLS PISKGFHTIP STDISMFTLS RDPSKLTMGT LLNSDRDHAF LQFHNSTPKE FKESLHNNPA NRRTTPV UniProtKB: Voltage-dependent calcium channel gamma-3 subunit |
-Macromolecule #3: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquino...
Macromolecule | Name: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid type: ligand / ID: 3 / Number of copies: 4 / Formula: ZK1 |
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Molecular weight | Theoretical: 409.254 Da |
Chemical component information | ![]() ChemComp-ZK1: |
-Macromolecule #4: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 4 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Macromolecule #5: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Macromolecule | Name: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / type: ligand / ID: 5 / Number of copies: 4 / Formula: OLC |
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Molecular weight | Theoretical: 356.54 Da |
Chemical component information | ![]() ChemComp-OLC: |
-Macromolecule #6: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 6 / Number of copies: 6 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ![]() ChemComp-POV: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 25 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Servalcat |
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Refinement | Space: RECIPROCAL |
Output model | ![]() PDB-8c1q: |