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9xjl

The LBD-TMD structure of homomeric GluA4 AMPA receptor

Method: ELECTRON MICROSCOPY Dmax: 136.8 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 415–843 Chain B； UniProt 415–843 Chain C； UniProt 415–843 Chain D； UniProt 415–843 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.80 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 9XJL 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 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
9XJM The ATD 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 21–401（381 aa）
Chain B 21–401（381 aa）
Chain C 21–401（381 aa）
Chain D 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 4.00 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 1–429； UniProt 415–843 Author chain B； PDBConstruct 1–429； UniProt 415–843 Author chain C； PDBConstruct 1–429； UniProt 415–843 Author chain D； PDBConstruct 1–429； UniProt 415–843

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 9xjl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9xjl
Deposition date deposition_date2025-11-04
Structure title titleThe LBD-TMD structure of homomeric GluA4 AMPA receptor
Keywords keywordsAMPA receptor, native, GluA1, GluA4, LBD, TMD, CNIH3, active state, MEMBRANE PROTEIN; 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_guinier42.79 Å
Radius of gyration Rg (electron density) rg_electron42.68 Å
Forward intensity I(0) i0436931000.00
Molecular weight molecular_weight181000.0 kDa
Excluded volume excluded_volume230740 ų
Envelope volume envelope_volume336690 ų
Hydration-shell volume shell_volume66370 ų
Envelope diameter envelope_diameter139.3 Å
Shell Rg shell_rg47.36 Å
Envelope Rg envelope_rg41.80 Å
Shape Rg shape_rg42.69 Å
Total Rg total_rg42.87 Å
Total atoms total_atoms12734
Residues n_residues1630
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 dmax136.8 Å
Rg (real space) rg_real42.70 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real4.3690e+08
I(0) uncertainty (real space) i0_real_error6.6200e+06
Rg (reciprocal space) rg_reciprocal42.79 Å
I(0) (reciprocal space) i0_reciprocal437000000.0000
Solution quality estimate total_estimate0.8970
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.4 Å
Skewness Skewness skewness0.205
Kurtosis Kurtosis kurtosis-0.605
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha126900000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.849
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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)