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- PDB-9qpw: GluA4, resting state, structure of TMD/LBD -

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Basic information

Entry
Database: PDB / ID: 9qpw
TitleGluA4, resting state, structure of TMD/LBD
ComponentsIsoform 2 of Glutamate receptor 4
KeywordsMEMBRANE PROTEIN / GluA4 / GRIA4 / TMD/LBD / Resting state / NBQX
Function / homology
Function and homology information


Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission, glutamatergic / response to fungicide / glutamate-gated receptor activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / chemical synaptic transmission / dendritic spine / postsynaptic density / neuronal cell body / dendrite / synapse / glutamatergic synapse / identical protein binding / 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
Chem-E2Q / Glutamate receptor 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsVega-Gutierrez, C. / Herguedas, B.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-106284GA-I00 Spain
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: GluA4 AMPA receptor gating mechanisms and modulation by auxiliary subunits
Authors: Vega-Gutierrez, C. / Herguedas, B. / Soto, D. / Sanchez-Valls, I. / Picanol-Parraga, J.
History
DepositionMar 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Glutamate receptor 4
B: Isoform 2 of Glutamate receptor 4
D: Isoform 2 of Glutamate receptor 4
C: Isoform 2 of Glutamate receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,0338
Polymers394,6884
Non-polymers1,3454
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Isoform 2 of Glutamate receptor 4 / GluR-4 / GluR4 / AMPA-selective glutamate receptor 4 / GluR-D / Glutamate receptor ionotropic / AMPA 4 / GluA4


Mass: 98671.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria4, Glur4 / Plasmid: pBICMam
Cell line (production host): Human embryonic kidney 293 cells
Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P19493
#2: 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 / 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: GluA4, resting state, structure of TMD/LBD / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsocium chlorideNaCl1
220 mMTris(hydroximethyl)aminomethanNH2C(CH2OH)31
30.02 %Glyco-diosgenin (GDN)C56H92O251
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was incubated with the AMPA receptor antagonist (NBQX) to capture the receptor in its resting state.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 25288

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Processing

EM software
IDNameVersionCategory
1RELION4.1particle selection
4RELION4.1CTF correction
7UCSF Chimera1.18model fitting
9PHENIX1.19.2_4158model refinement
12RELION4.1classification
13RELION4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59714 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: The TMD region of GluA4:G2restI and four GluA2 LBD monomers (PDB 3UA8) were rigid body fitted in Chimera. Manual model building, refinement and validation were performed using Refmac 5 ...Details: The TMD region of GluA4:G2restI and four GluA2 LBD monomers (PDB 3UA8) were rigid body fitted in Chimera. Manual model building, refinement and validation were performed using Refmac 5 Servalcat followed by model building in Coot and Real Space Refinement in Phenix.
Atomic model building

3D fitting-ID: 1 / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-IDSource nameDetails
13UA8

3ua8

3UA81PDB
2OtherOur TMD region of GluA4:G2restI
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212304
ELECTRON MICROSCOPYf_angle_d0.58516660
ELECTRON MICROSCOPYf_dihedral_angle_d4.1121720
ELECTRON MICROSCOPYf_chiral_restr0.0411874
ELECTRON MICROSCOPYf_plane_restr0.0082042

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