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- PDB-9j94: Native GluA1/GluA4-CNIH3 complex in active state -

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Basic information

Entry
Database: PDB / ID: 9j94
TitleNative GluA1/GluA4-CNIH3 complex in active state
Components
  • (Glutamate receptor) x 2
  • Cornichon family AMPA receptor auxiliary protein 3
KeywordsMEMBRANE PROTEIN / AMPA receptor / native / GluA1 / GluA4 / LBD / TMD / CNIH3 / active state
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 / vesicle-mediated transport / 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 / recycling endosome / receptor internalization / postsynaptic density membrane / modulation of chemical synaptic transmission / synaptic vesicle membrane / dendritic spine / signaling receptor binding / neuronal cell body / dendrite / synapse / glutamatergic synapse / cell surface / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / 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 ...Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / 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
: / GAMMA-L-GLUTAMIC ACID / Glutamate receptor / Cornichon family AMPA receptor auxiliary protein 3 / Glutamate receptor
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsLi, X. / Li, R. / Wei, Y. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92157102 China
CitationJournal: To Be Published
Title: Native GluA1/GluA4-CNIH3 complex in active state
Authors: Li, X. / Li, R. / Wei, Y. / Zhao, Y.
History
DepositionAug 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Cornichon family AMPA receptor auxiliary protein 3
E: Cornichon family AMPA receptor auxiliary protein 3
G: Cornichon family AMPA receptor auxiliary protein 3
H: Cornichon family AMPA receptor auxiliary protein 3
A: Glutamate receptor
B: Glutamate receptor
D: Glutamate receptor
C: Glutamate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,51316
Polymers477,3658
Non-polymers2,1488
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cornichon family AMPA receptor auxiliary protein 3


Mass: 18863.311 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BJP0
#2: Protein Glutamate receptor


Mass: 101565.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZS63
#3: Protein Glutamate receptor


Mass: 99389.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L8N9
#4: Chemical
ChemComp-GGL / GAMMA-L-GLUTAMIC ACID / L-GLUTAMIC ACID


Type: L-gamma-peptide, C-delta linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-A1EA4 / (3~{R})-3-[(1~{S},2~{S},4~{S})-2-bicyclo[2.2.1]hept-5-enyl]-6-chloranyl-1,1-bis(oxidanylidene)-3,4-dihydro-2~{H}-1$l^{6},2,4-benzothiadiazine-7-sulfonamide


Mass: 389.878 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16ClN3O4S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: native GluA1/GluA4-CNIH3 complex in active state / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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 / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90079 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217318
ELECTRON MICROSCOPYf_angle_d0.49623428
ELECTRON MICROSCOPYf_dihedral_angle_d4.0572364
ELECTRON MICROSCOPYf_chiral_restr0.0372590
ELECTRON MICROSCOPYf_plane_restr0.0032854

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