9rl5

a5b3 GABAAR bound to Topiramate, GABA, and Mb25 in a desensitized state in saposin nanodiscs

Method: ELECTRON MICROSCOPY Dmax: 127.0 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5

Homo sapiens

UniProt P31644

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 其他Polymer 9 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 33–346 Chain A; UniProt 421–462 Chain D; UniProt 33–346 Chain D; UniProt 421–462 Not recorded Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein × 3 (P28472,P42212) Megabody 25 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ABU GAMMA-AMINO-BUTANOIC ACID × 2 TOR [(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

22 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBRA5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 317–630; UniProt 33–346 Author chain A; PDBConstruct 638–679; UniProt 421–462 Author chain D; PDBConstruct 317–630; UniProt 33–346 Author chain D; PDBConstruct 638–679; UniProt 421–462

Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein

Homo sapiens

UniProt P28472

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 其他Polymer 9 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–332 Chain B; UniProt 447–473 Chain C; UniProt 1–332 Chain C; UniProt 447–473 Chain E; UniProt 1–332 Chain E; UniProt 447–473 Not recorded Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5 × 2 (P31644) Megabody 25 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ABU GAMMA-AMINO-BUTANOIC ACID × 2 TOR [(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

94 other PDB entries and 94 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBRB3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–332; UniProt 1–332 Author chain B; PDBConstruct 582–608; UniProt 447–473 Author chain C; PDBConstruct 1–332; UniProt 1–332 Author chain C; PDBConstruct 582–608; UniProt 447–473 Author chain E; PDBConstruct 1–332; UniProt 1–332 Author chain E; PDBConstruct 582–608; UniProt 447–473

Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein

Homo sapiens

UniProt P42212

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 其他Polymer 9 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–238 Chain C; UniProt 2–238 Chain E; UniProt 2–238 Not recorded Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5 × 2 (P31644) Megabody 25 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ABU GAMMA-AMINO-BUTANOIC ACID × 2 TOR [(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

568 other PDB entries and 744 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GFP_AEQVI
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 341–577; UniProt 2–238 Author chain C; PDBConstruct 341–577; UniProt 2–238 Author chain E; PDBConstruct 341–577; UniProt 2–238

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 9rl5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9rl5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9rl5
Deposition date deposition_date2025-06-16
Structure title titlea5b3 GABAAR bound to Topiramate, GABA, and Mb25 in a desensitized state in saposin nanodiscs
Keywords keywordsGABAA receptor, pentameric ligand gated ion channel, ion channel, anticonvulsant, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.38
Radius of gyration Rg (electron density) rg_electron38.92
Forward intensity I(0) i0639435000.00
Molecular weight molecular_weight216030.0 kDa
Excluded volume excluded_volume273760 ų
Envelope volume envelope_volume349520 ų
Hydration-shell volume shell_volume72741 ų
Envelope diameter envelope_diameter132.5
Shell Rg shell_rg46.52
Envelope Rg envelope_rg38.42
Shape Rg shape_rg38.95
Total Rg total_rg39.23
Total atoms total_atoms15218
Residues n_residues1816
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.0
Rg (real space) rg_real39.20
Rg uncertainty (real space) rg_real_error0.79
I(0) (real space) i0_real6.3940e+08
I(0) uncertainty (real space) i0_real_error1.0610e+07
Rg (reciprocal space) rg_reciprocal39.32
I(0) (reciprocal space) i0_reciprocal639500000.0000
Solution quality estimate total_estimate0.8857
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.6
Skewness Skewness skewness0.243
Kurtosis Kurtosis kurtosis-0.373
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha97430000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (13)

8. Citations (1)

9. Files and Curves (10)