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- PDB-9nr8: The structure of cerebellar GluA1/A4 ATD -

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Basic information

Entry
Database: PDB / ID: 9nr8
TitleThe structure of cerebellar GluA1/A4 ATD
Components
  • (Glutamate receptor ...) x 2
  • 11B8 scFv
KeywordsMEMBRANE PROTEIN / iGluR / CP-AMPA receptors
Function / homology
Function and homology information


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 / cellular response to ammonium ion / response to sucrose / proximal dendrite / myosin V binding ...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 / cellular response to ammonium ion / response to sucrose / proximal dendrite / myosin V binding / neuron spine / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / cellular response to L-glutamate / regulation of monoatomic ion transmembrane transport / conditioned place preference / response to arsenic-containing substance / cellular response to dsRNA / regulation of synapse structure or activity / dendritic spine membrane / Synaptic adhesion-like molecules / long-term synaptic depression / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / response to morphine / neuronal cell body membrane / peptide hormone receptor binding / protein kinase A binding / response to psychosocial stress / spinal cord development / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / : / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / behavioral response to pain / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / adenylate cyclase binding / asymmetric synapse / regulation of receptor recycling / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / long-term memory / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / response to electrical stimulus / neuronal action potential / glutamate-gated receptor activity / response to fungicide / synapse assembly / presynaptic active zone membrane / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / cellular response to amino acid stimulus / response to cocaine / synaptic membrane / response to nutrient levels / modulation of chemical synaptic transmission / postsynaptic density membrane / : / terminal bouton / neuromuscular junction / cellular response to growth factor stimulus / recycling endosome / cerebral cortex development / regulation of synaptic plasticity / small GTPase binding / receptor internalization / response to peptide hormone / long-term synaptic potentiation / response to toxic substance / synaptic vesicle membrane / recycling endosome membrane / synaptic vesicle / cell-cell junction / G-protein beta-subunit binding / response to estradiol / presynapse / amyloid-beta binding / presynaptic membrane / cell body / early endosome membrane / scaffold protein binding / chemical synaptic transmission / dendritic spine
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 1 / Glutamate receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsFang, C.F. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: Gating and noelin clustering of native Ca2+-permeable AMPA receptors
Authors: Fang, C. / Spangler, C.J. / Park, J. / Sheldon, N. / Trussell, L.O. / Gouaux, E.
History
DepositionMar 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: 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 1
B: Glutamate receptor 4
C: Glutamate receptor 1
D: Glutamate receptor 4
E: 11B8 scFv
F: 11B8 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,71718
Polymers227,1126
Non-polymers4,60412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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 / AMPA 1


Mass: 42956.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P19490
#2: Protein Glutamate receptor 4 / GluR-4 / GluR4 / AMPA-selective glutamate receptor 4 / GluR-D / Glutamate receptor ionotropic / AMPA 4 / GluA4


Mass: 43087.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P19493

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Antibody , 1 types, 2 molecules EF

#3: Antibody 11B8 scFv


Mass: 27511.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)

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Sugars , 3 types, 12 molecules

#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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.: 4 / 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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Details

Has ligand of interestN
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: CP-AMPA receptors / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 8
SpecimenConc.: 0.1 mg/ml / Embedding 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: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36405 / Symmetry type: POINT
RefinementHighest resolution: 3.53 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414871
ELECTRON MICROSCOPYf_angle_d0.64720215
ELECTRON MICROSCOPYf_dihedral_angle_d5.9632241
ELECTRON MICROSCOPYf_chiral_restr0.0442345
ELECTRON MICROSCOPYf_plane_restr0.0052647

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