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- PDB-9x58: The GluA4-ATD in Complex with the 1D8-Fab -

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Basic information

Entry
Database: PDB / ID: 9x58
TitleThe GluA4-ATD in Complex with the 1D8-Fab
Components
  • Glutamate receptor 4
  • Heavy Chain of 1D8 Fab
  • Light Chain of 1D8 Fab
KeywordsMEMBRANE PROTEIN / AMPA receptor / native / GluA1 / GluA4 / LBD / TMD / CNIH3 / active state / 1D8
Function / homology
Function and homology information


Activation of AMPA receptors / Synaptic adhesion-like molecules / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / positive regulation of synaptic transmission, glutamatergic ...Activation of AMPA receptors / Synaptic adhesion-like molecules / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / positive regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / presynaptic active zone membrane / 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 / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / dendritic spine / chemical synaptic transmission / postsynaptic density / neuronal cell body / synapse / dendrite / 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
Glutamate receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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: Cell Res. / Year: 2026
Title: Assembly and gating mechanism of native AMPA receptors from the cerebellum
Authors: Li, X. / Li, R. / Wei, Y. / Chen, J. / Zhao, J. / Zhao, J. / Wang, W. / Li, N. / Wang, L. / Hu, T. / Dong, Y. / Zhu, Y. / Wei, C. / Li, L. / Zhang, W. / Huang, Z. / Zhao, Y.
History
DepositionOct 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 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
A: Glutamate receptor 4
B: Glutamate receptor 4
L: Light Chain of 1D8 Fab
D: Light Chain of 1D8 Fab
C: Heavy Chain of 1D8 Fab
H: Heavy Chain of 1D8 Fab


Theoretical massNumber of molelcules
Total (without water)160,5496
Polymers160,5496
Non-polymers00
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 Glutamate receptor 4 / GluR-4 / GluR4 / AMPA-selective glutamate receptor 4 / GluR-D / Glutamate receptor ionotropic / AMPA 4 / GluA4


Mass: 43388.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gria4, Glur4 / Production host: Homo sapiens (human) / References: UniProt: Q9Z2W8
#2: Antibody Light Chain of 1D8 Fab


Mass: 18400.619 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Heavy Chain of 1D8 Fab


Mass: 18485.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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: The GluA4-ATD in Complex with the 1D8-Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus abbotti (Abbott's mouse)
Source (recombinant)Organism: Homo (humans)
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: TFS 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 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182287 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410524
ELECTRON MICROSCOPYf_angle_d0.59514444
ELECTRON MICROSCOPYf_dihedral_angle_d4.661692
ELECTRON MICROSCOPYf_chiral_restr0.0421780
ELECTRON MICROSCOPYf_plane_restr0.0031952

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