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9xjm

The ATD structure of homomeric GluA4 AMPA receptor

Method: ELECTRON MICROSCOPY Dmax: 153.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate receptor 4

Mus musculus

UniProt Q9Z2W8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 21–401 Chain B； UniProt 21–401 Chain C； UniProt 21–401 Chain D； UniProt 21–401 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9XJM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9X57 The LBD-TMD structure of GluA4-1D8 complex Deposited 2025-10-12 Different construct Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 415–843（429 aa）
Chain B 415–843（429 aa）
Chain C 415–843（429 aa）
Chain D 415–843（429 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9X58 The GluA4-ATD in Complex with the 1D8-Fab Deposited 2025-10-12 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 21–401（381 aa）
Chain B 21–401（381 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9XJL The LBD-TMD structure of homomeric GluA4 AMPA receptor Deposited 2025-11-04 Different construct Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 415–843（429 aa）
Chain B 415–843（429 aa）
Chain C 415–843（429 aa）
Chain D 415–843（429 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GRIA4_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–381； UniProt 21–401 Author chain B； PDBConstruct 1–381； UniProt 21–401 Author chain C； PDBConstruct 1–381； UniProt 21–401 Author chain D； PDBConstruct 1–381； UniProt 21–401

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9xjm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xjm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9xjm
Deposition date deposition_date2025-11-04
Structure title titleThe ATD structure of homomeric GluA4 AMPA receptor
Keywords keywordsAMPA receptor, native, GluA1, GluA4, LBD, TMD, CNIH3, active state, MEMBRANE PROTEIN, 1D8; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.25 Å
Radius of gyration Rg (electron density) rg_electron47.19 Å
Forward intensity I(0) i0426930000.00
Molecular weight molecular_weight171620.0 kDa
Excluded volume excluded_volume215150 ų
Envelope volume envelope_volume317680 ų
Hydration-shell volume shell_volume57509 ų
Envelope diameter envelope_diameter161.2 Å
Shell Rg shell_rg49.85 Å
Envelope Rg envelope_rg45.90 Å
Shape Rg shape_rg47.18 Å
Total Rg total_rg47.32 Å
Total atoms total_atoms12112
Residues n_residues1508
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax153.6 Å
Rg (real space) rg_real47.48 Å
Rg uncertainty (real space) rg_real_error1.50 Å
I(0) (real space) i0_real4.2690e+08
I(0) uncertainty (real space) i0_real_error8.6540e+06
Rg (reciprocal space) rg_reciprocal47.26 Å
I(0) (reciprocal space) i0_reciprocal426800000.0000
Solution quality estimate total_estimate0.8517
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.5 Å
Skewness Skewness skewness0.340
Kurtosis Kurtosis kurtosis-0.660
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48020000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.425
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)