9ffl

Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived symmetric bound-closed state

Method: ELECTRON MICROSCOPY Dmax: 126.8 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 × 6 其他Polymer 8 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 32–339 Chain A; UniProt 418–456 Chain D; UniProt 32–339 Chain D; UniProt 418–456 Not recorded Gamma-aminobutyric acid receptor subunit beta-3 × 3 (P28472) Megabody25,Outer membrane protein × 1 (B5Z8H1) ;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 ; × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 D10 DECANE × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 CL CHLORIDE ION × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 2 R16 HEXADECANE × 1 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 2.80 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.

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 58–365; UniProt 32–339 Author chain A; PDBConstruct 373–411; UniProt 418–456 Author chain D; PDBConstruct 58–365; UniProt 32–339 Author chain D; PDBConstruct 373–411; UniProt 418–456

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 × 6 其他Polymer 8 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 26–332 Chain B; UniProt 447–473 Chain C; UniProt 26–332 Chain C; UniProt 447–473 Chain E; UniProt 26–332 Chain E; UniProt 447–473 Not recorded Gamma-aminobutyric acid receptor subunit alpha-1 × 2 (P14867) Megabody25,Outer membrane protein × 1 (B5Z8H1) ;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 ; × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 D10 DECANE × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 CL CHLORIDE ION × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 2 R16 HEXADECANE × 1 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 2.80 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.

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 55–361; UniProt 26–332 Author chain B; PDBConstruct 369–395; UniProt 447–473 Author chain C; PDBConstruct 55–361; UniProt 26–332 Author chain C; PDBConstruct 369–395; UniProt 447–473 Author chain E; PDBConstruct 55–361; UniProt 26–332 Author chain E; PDBConstruct 369–395; UniProt 447–473

Megabody25,Outer membrane protein

Lama glama

UniProt B5Z8H1

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 × 6 其他Polymer 8 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 226–446 Chain F; UniProt 53–221 Not recorded Gamma-aminobutyric acid receptor subunit alpha-1 × 2 (P14867) Gamma-aminobutyric acid receptor subunit beta-3 × 3 (P28472) ;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 ; × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 D10 DECANE × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 CL CHLORIDE ION × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 2 R16 HEXADECANE × 1 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 2.80 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.

22 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B5Z8H1_HELPG
Isoform
PDB entities 3
Chains and sequence ranges Author chain F; PDBConstruct 13–233; UniProt 226–446 Author chain F; PDBConstruct 234–402; UniProt 53–221

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 9ffl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9ffl
Deposition date deposition_date2024-05-23
Structure title titleCryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived symmetric bound-closed 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_guinier39.01
Radius of gyration Rg (electron density) rg_electron38.71
Forward intensity I(0) i0608742000.00
Molecular weight molecular_weight214230.0 kDa
Excluded volume excluded_volume273000 ų
Envelope volume envelope_volume344480 ų
Hydration-shell volume shell_volume72079 ų
Envelope diameter envelope_diameter125.5
Shell Rg shell_rg46.27
Envelope Rg envelope_rg38.22
Shape Rg shape_rg38.74
Total Rg total_rg39.02
Total atoms total_atoms15094
Residues n_residues1784
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 dmax126.8
Rg (real space) rg_real38.86
Rg uncertainty (real space) rg_real_error0.82
I(0) (real space) i0_real6.0870e+08
I(0) uncertainty (real space) i0_real_error9.9730e+06
Rg (reciprocal space) rg_reciprocal38.96
I(0) (reciprocal space) i0_reciprocal608800000.0000
Solution quality estimate total_estimate0.8848
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.4
Skewness Skewness skewness0.264
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha119300000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.920

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

8. Citations (1)

9. Files and Curves (10)