5osc

GLIC-GABAAR alpha1 chimera crystallized in complex with pregnenolone sulfate at pH 4.5

Method: X-RAY DIFFRACTION Dmax: 123.5 Å Quality: GOOD

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

Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1

Mus musculus

UniProt P26048

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 Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 251–339 Chain B; UniProt 251–339 Chain C; UniProt 251–339 Chain D; UniProt 251–339 Chain E; UniProt 251–339 Not recorded ACT ACETATE ION × 8 CL CHLORIDE ION × 5 A8W Pregnenolone sulfate × 5 Y01 CHOLESTEROL HEMISUCCINATE × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;289 K;12-16% PEG 4000, 100 mM NaCl, 100 mM Li2S04, 100 mM sodium acetate pH 4-5 Resolution 3.10 Å R-free 0.246

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name GBRA2_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 194–282; UniProt 251–339 Author chain B; PDBConstruct 194–282; UniProt 251–339 Author chain C; PDBConstruct 194–282; UniProt 251–339 Author chain D; PDBConstruct 194–282; UniProt 251–339 Author chain E; PDBConstruct 194–282; UniProt 251–339

Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1

Mus musculus

UniProt P62812

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 Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 417–455 Chain B; UniProt 417–455 Chain C; UniProt 417–455 Chain D; UniProt 417–455 Chain E; UniProt 417–455 Not recorded ACT ACETATE ION × 8 CL CHLORIDE ION × 5 A8W Pregnenolone sulfate × 5 Y01 CHOLESTEROL HEMISUCCINATE × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;289 K;12-16% PEG 4000, 100 mM NaCl, 100 mM Li2S04, 100 mM sodium acetate pH 4-5 Resolution 3.10 Å R-free 0.246

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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBRA1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 290–328; UniProt 417–455 Author chain B; PDBConstruct 290–328; UniProt 417–455 Author chain C; PDBConstruct 290–328; UniProt 417–455 Author chain D; PDBConstruct 290–328; UniProt 417–455 Author chain E; PDBConstruct 290–328; UniProt 417–455

Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1

Mus musculus

UniProt Q7NDN8

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 Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 44–236 Chain B; UniProt 44–236 Chain C; UniProt 44–236 Chain D; UniProt 44–236 Chain E; UniProt 44–236 Not recorded ACT ACETATE ION × 8 CL CHLORIDE ION × 5 A8W Pregnenolone sulfate × 5 Y01 CHOLESTEROL HEMISUCCINATE × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;289 K;12-16% PEG 4000, 100 mM NaCl, 100 mM Li2S04, 100 mM sodium acetate pH 4-5 Resolution 3.10 Å R-free 0.246

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.

129 other PDB entries and 135 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLIC_GLOVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–193; UniProt 44–236 Author chain B; PDBConstruct 1–193; UniProt 44–236 Author chain C; PDBConstruct 1–193; UniProt 44–236 Author chain D; PDBConstruct 1–193; UniProt 44–236 Author chain E; PDBConstruct 1–193; UniProt 44–236

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 5osc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5osc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5osc
Deposition date deposition_date2017-08-17
Structure title titleGLIC-GABAAR alpha1 chimera crystallized in complex with pregnenolone sulfate at pH 4.5
Keywords keywordsGABAA-receptor ion channel Ion transport Extracellular ligand gated ion channel, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.97
Radius of gyration Rg (electron density) rg_electron37.44
Forward intensity I(0) i0416033000.00
Molecular weight molecular_weight180580.0 kDa
Excluded volume excluded_volume231560 ų
Envelope volume envelope_volume293070 ų
Hydration-shell volume shell_volume64046 ų
Envelope diameter envelope_diameter125.4
Shell Rg shell_rg44.79
Envelope Rg envelope_rg37.03
Shape Rg shape_rg37.43
Total Rg total_rg37.91
Total atoms total_atoms13188
Residues n_residues1560
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 dmax123.5
Rg (real space) rg_real37.87
Rg uncertainty (real space) rg_real_error1.16
I(0) (real space) i0_real4.1600e+08
I(0) uncertainty (real space) i0_real_error7.0210e+06
Rg (reciprocal space) rg_reciprocal37.94
I(0) (reciprocal space) i0_reciprocal416100000.0000
Solution quality estimate total_estimate0.8793
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.0
Skewness Skewness skewness0.312
Kurtosis Kurtosis kurtosis-0.307
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha57020000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.892

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id5oscA01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5oscA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id5oscB01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5oscB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id5oscC01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5oscC02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id5oscD01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5oscD02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id5oscE01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id5oscE02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain

8. Citations (1)

9. Files and Curves (10)