9fg9

Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in complex with GABA and Etomidate in the long-lived symmetric desensitised state

Method: ELECTRON MICROSCOPY Dmax: 127.7 Å Quality: GOOD

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

Gamma-aminobutyric acid receptor subunit alpha-1

Homo sapiens

UniProt P14867

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 7 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 28–456 Chain D; UniProt 28–456 Not recorded Gamma-aminobutyric acid receptor subunit beta-3 × 2 (P28472) Gamma-aminobutyric acid receptor subunit gamma-2 × 1 (P18507) ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CL CHLORIDE ION × 3 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 D10 DECANE × 5 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 2 R16 HEXADECANE × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 2 V8D Etomidate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.70 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.

83 other PDB entries and 85 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBRA1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 36–464; UniProt 28–456 Author chain D; PDBConstruct 36–464; UniProt 28–456

Gamma-aminobutyric acid receptor subunit beta-3

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 Other combination Heteromer Protein × 5 其他Polymer 7 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 1–473 Chain E; UniProt 1–473 Not recorded Gamma-aminobutyric acid receptor subunit alpha-1 × 2 (P14867) Gamma-aminobutyric acid receptor subunit gamma-2 × 1 (P18507) ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CL CHLORIDE ION × 3 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 D10 DECANE × 5 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 2 R16 HEXADECANE × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 2 V8D Etomidate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.70 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 P28472-2
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–473; UniProt 1–473 Author chain E; PDBConstruct 1–473; UniProt 1–473

Gamma-aminobutyric acid receptor subunit gamma-2

Homo sapiens

UniProt P18507

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 7 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–475 Not recorded Gamma-aminobutyric acid receptor subunit alpha-1 × 2 (P14867) Gamma-aminobutyric acid receptor subunit beta-3 × 2 (P28472) ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CL CHLORIDE ION × 3 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 D10 DECANE × 5 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 2 R16 HEXADECANE × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 2 V8D Etomidate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.70 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.

70 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBRG2_HUMAN
Isoform P18507-2
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–475; UniProt 1–475

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 9fg9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9fg9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9fg9
Deposition date deposition_date2024-05-23
Structure title titleCryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in complex with GABA and Etomidate in the long-lived symmetric desensitised state
Keywords keywordsGABA, neurotransmission, gating cycle, time-resolved cryo-EM, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.99
Radius of gyration Rg (electron density) rg_electron38.61
Forward intensity I(0) i0575562000.00
Molecular weight molecular_weight208650.0 kDa
Excluded volume excluded_volume266020 ų
Envelope volume envelope_volume327070 ų
Hydration-shell volume shell_volume69199 ų
Envelope diameter envelope_diameter131.7
Shell Rg shell_rg45.69
Envelope Rg envelope_rg38.30
Shape Rg shape_rg38.62
Total Rg total_rg38.98
Total atoms total_atoms14690
Residues n_residues1710
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 dmax127.7
Rg (real space) rg_real38.97
Rg uncertainty (real space) rg_real_error0.83
I(0) (real space) i0_real5.7560e+08
I(0) uncertainty (real space) i0_real_error9.4160e+06
Rg (reciprocal space) rg_reciprocal38.98
I(0) (reciprocal space) i0_reciprocal575600000.0000
Solution quality estimate total_estimate0.8673
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.7
Skewness Skewness skewness0.391
Kurtosis Kurtosis kurtosis-0.261
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha103000000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.776

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (15)

8. Citations (1)

9. Files and Curves (10)