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- PDB-7oca: Resting state full-length GluA1/A2 heterotertramer in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7oca
TitleResting state full-length GluA1/A2 heterotertramer in complex with TARP gamma 8 and CNIH2
Components
  • (Glutamate receptor ...) x 2
  • Protein cornichon homolog 2
  • Voltage-dependent calcium channel gamma-8 subunit
KeywordsMEMBRANE PROTEIN / AMPAR / ion channels / neurotransmission
Function / homology
Function and homology information


negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior ...negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior / localization within membrane / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / cellular response to ammonium ion / neurotransmitter receptor transport, postsynaptic endosome to lysosome / neurotransmitter receptor internalization / response to sucrose / L-type voltage-gated calcium channel complex / LGI-ADAM interactions / proximal dendrite / myosin V binding / Trafficking of AMPA receptors / neuron spine / cellular response to L-glutamate / regulation of AMPA receptor activity / regulation of monoatomic ion transmembrane transport / protein phosphatase 2B binding / response to arsenic-containing substance / postsynaptic neurotransmitter receptor diffusion trapping / conditioned place preference / regulation of NMDA receptor activity / cellular response to dsRNA / dendritic spine membrane / Synaptic adhesion-like molecules / beta-2 adrenergic receptor binding / long-term synaptic depression / cellular response to peptide hormone stimulus / response to morphine / protein kinase A binding / neuronal cell body membrane / peptide hormone receptor binding / spine synapse / dendritic spine neck / response to psychosocial stress / spinal cord development / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / channel regulator activity / transmission of nerve impulse / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / behavioral response to pain / kainate selective glutamate receptor activity / adenylate cyclase binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / positive regulation of excitatory postsynaptic potential / excitatory synapse / : / asymmetric synapse / regulation of receptor recycling / calcium channel regulator activity / regulation of postsynaptic membrane potential / G-protein alpha-subunit binding / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / positive regulation of synaptic transmission / glutamate receptor binding / postsynaptic density, intracellular component / voltage-gated calcium channel activity / extracellular ligand-gated monoatomic ion channel activity / neuronal action potential / response to electrical stimulus / synapse assembly / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / vesicle-mediated transport / dendrite membrane / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / ionotropic glutamate receptor binding / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
Similarity search - Function
Voltage-dependent calcium channel, gamma-8 subunit / Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit ...Voltage-dependent calcium channel, gamma-8 subunit / Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / Chem-E2Q / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Glutamate receptor 1 / Glutamate receptor 2 / Protein cornichon homolog 2 / Voltage-dependent calcium channel gamma-8 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang, D. / Watson, J.F. / Matthews, P.M. / Cais, O. / Greger, I.H.
Funding support2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105174197
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N002113/1
CitationJournal: Nature / Year: 2021
Title: Gating and modulation of a hetero-octameric AMPA glutamate receptor.
Authors: Danyang Zhang / Jake F Watson / Peter M Matthews / Ondrej Cais / Ingo H Greger /
Abstract: AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning. A diverse array of AMPAR signalling complexes are ...AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1-GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties.
History
DepositionApr 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 30, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entity_branch_descriptor / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Glutamate receptor 1
B: Glutamate receptor 2
G: Protein cornichon homolog 2
I: Voltage-dependent calcium channel gamma-8 subunit
D: Glutamate receptor 2
J: Voltage-dependent calcium channel gamma-8 subunit
C: Glutamate receptor 1
E: Protein cornichon homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,63472
Polymers528,9718
Non-polymers42,66364
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Glutamate receptor ... , 2 types, 4 molecules ACBD

#1: Protein Glutamate receptor 1 / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / ...GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / AMPA 1 / GluA1


Mass: 102661.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria1, Glur1 / Production host: Homo sapiens (human) / References: UniProt: P19490
#2: Protein Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 96247.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Homo sapiens (human) / References: UniProt: P19491

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Protein , 2 types, 4 molecules GEIJ

#3: Protein Protein cornichon homolog 2 / CNIH-2 / Cornichon family AMPA receptor auxiliary protein 2 / Cornichon-like protein


Mass: 22000.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cnih2 / Production host: Homo sapiens (human) / References: UniProt: Q5BJU5
#4: Protein Voltage-dependent calcium channel gamma-8 subunit / Neuronal voltage-gated calcium channel gamma-8 subunit / Transmembrane AMPAR regulatory protein ...Neuronal voltage-gated calcium channel gamma-8 subunit / Transmembrane AMPAR regulatory protein gamma-8 / TARP gamma-8


Mass: 43576.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacng8 / Production host: Homo sapiens (human) / References: UniProt: Q8VHW5

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Sugars , 3 types, 12 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 52 molecules

#7: Chemical
ChemComp-E2Q / 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide


Mass: 336.280 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8N4O6S / Comment: antagonist*YM
#9: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#10: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GluA1/A2 heterotertramer in complex with auxiliary subunits TARP gamma 8 and CNIH2
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.527 MDa
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218320 / Symmetry type: POINT

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