SAXSdb — 7cdb

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

Gamma-aminobutyric acid receptor-associated protein-like 1

Mus musculus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–117	Not recorded	CIT CITRIC ACID × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；289 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate pH 5.6, and 30% PEG 4000	Resolution 1.95 Å R-free 0.232
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–117	Not recorded	Gamma-aminobutyric acid receptor subunit gamma-2 × 1 （P22723） CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；289 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate pH 5.6, and 30% PEG 4000	Resolution 1.95 Å R-free 0.232

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 7CDB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YIP Crystal Structure of AnkG LIR/GABARAPL1 complex Deposited 2017-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–117（117 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；289 K；35% w/v Pentaerythritol ethoxylate 797 (15/4 EO/OH), 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6)	Resolution 1.85 Å R-free 0.222

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GBRL1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–123； UniProt 1–117 Author chain B； PDBConstruct 7–123； UniProt 1–117

Gamma-aminobutyric acid receptor subunit gamma-2

Mus musculus

UniProt P22723

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 406–423	Not recorded	Gamma-aminobutyric acid receptor-associated protein-like 1 × 1 （Q8R3R8） CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；289 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate pH 5.6, and 30% PEG 4000	Resolution 1.95 Å R-free 0.232

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 7CDB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8FOI Native GABA-A receptor from the mouse brain, alpha1-beta2-gamma2 subtype, in complex with GABA and allopregnanolone Deposited 2022-12-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain D 1–474（474 aa）	Not recorded	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 D12 DODECANE × 17 OCT N-OCTANE × 17 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 5 ABU GAMMA-AMINO-BUTANOIC ACID × 2 Y4B allopregnanolone × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
8G4N Native GABA-A receptor from the mouse brain, alpha1-beta2-gamma2 subtype, in complex with GABA, Zolpidem, and endogenous neurosteroids Deposited 2023-02-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain D 1–474（474 aa）	Not recorded	Y4B allopregnanolone × 2 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 D12 DODECANE × 17 OCT N-OCTANE × 17 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 5 ABU GAMMA-AMINO-BUTANOIC ACID × 2 R5R Zolpidem × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å
8G4O Native GABA-A receptor from the mouse brain, alpha1-beta2-gamma2 subtype, in complex with didesethylflurazepam and endogenous GABA Deposited 2023-02-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain D 1–474（474 aa）	Not recorded	ABU GAMMA-AMINO-BUTANOIC ACID × 2 YNL (5M)-1-(2-aminoethyl)-7-chloro-5-(2-fluorophenyl)-1,3-dihydro-2H-1,4-benzodiazepin-2-one × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.06 Å
8G4X Native GABA-A receptor from the mouse brain, meta-alpha1-alpha3-beta2-gamma2 subtype, in complex with GABA and allopregnanolone Deposited 2023-02-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–474（474 aa）	Not recorded	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 ABU GAMMA-AMINO-BUTANOIC ACID × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Y4B allopregnanolone × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.56 Å
8G5F Native GABA-A receptor from the mouse brain, ortho-alpha1-alpha3-beta2-gamma2 subtype, in complex with GABA and allopregnanolone Deposited 2023-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–474（474 aa）	Not recorded	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 Y4B allopregnanolone × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
8G5G Native GABA-A receptor from the mouse brain, meta-alpha1-alpha3-beta2-gamma2 subtype, in complex with GABA, Zolpidem, and endogenous neurosteroid Deposited 2023-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–474（474 aa）	Not recorded	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 Y4B allopregnanolone × 1 ABU GAMMA-AMINO-BUTANOIC ACID × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 R5R Zolpidem × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8G5H Native GABA-A receptor from the mouse brain, ortho-alpha1-alpha3-beta2-gamma2 subtype, in complex with GABA, Zolpidem, and endogenous neurosteroid Deposited 2023-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–474（474 aa）	Not recorded	ABU GAMMA-AMINO-BUTANOIC ACID × 2 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 R5R Zolpidem × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Y4B allopregnanolone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GBRG2_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–18； UniProt 406–423

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7cdb
Deposition date deposition_date	2020-06-19
Structure title title	Structure of GABARAPL1 in complex with GABA(A) receptor gamma 2
Keywords keywords	Protein binding; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	21.21 Å
Radius of gyration Rg (electron density) rg_electron	20.20 Å
Forward intensity I(0) i0	15386100.00
Molecular weight molecular_weight	30205.0 kDa
Excluded volume excluded_volume	37999 Å³
Envelope volume envelope_volume	45121 Å³
Hydration-shell volume shell_volume	18917 Å³
Envelope diameter envelope_diameter	71.2 Å
Shell Rg shell_rg	26.12 Å
Envelope Rg envelope_rg	20.34 Å
Shape Rg shape_rg	20.17 Å
Total Rg total_rg	21.14 Å
Total atoms total_atoms	2141
Residues n_residues	259
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	68.9 Å
Rg (real space) rg_real	21.17 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	1.5390e+07
I(0) uncertainty (real space) i0_real_error	1.5740e+05
Rg (reciprocal space) rg_reciprocal	21.18 Å
I(0) (reciprocal space) i0_reciprocal	15390000.0000
Solution quality estimate total_estimate	0.8963
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.523
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0003
Highest regularization parameter α highest_alpha	3097000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Gamma-aminobutyric acid receptor-associated protein-like 1
Molecular weight formula_weight	14642.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2244

GPGSEFMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Gamma-aminobutyric acid receptor subunit gamma-2
Molecular weight formula_weight	2084.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ERDEEYGYECLDGKDCAS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d7cdba1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.3 — GABARAP-like

Domain ID domain_id	d7cdba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d7cdbb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.3 — GABARAP-like

Domain ID domain_id	d7cdbb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (1)

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Unit-cell length a length_a	89.379 Å
Unit-cell length b length_b	89.379 Å
Unit-cell length c length_c	115.004 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.949 Å
Low-resolution limit resolution_low	36.681 Å
R factor r_factor	0.1991
R_work r_work	0.1974
R_free r_free	0.2315

fit	/app/data/saxs_computation/cd/7cdb/7cdb.fit
pddf	/app/data/pr_computation/cd/7cdb/7cdb.pr.out
profile	/app/data/saxs_computation/cd/7cdb/7cdb.dat

Structure of GABARAPL1 in complex with GABA(A) receptor gamma 2

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

Gamma-aminobutyric acid receptor-associated protein-like 1

State in the Current Structure

Other States of the Same Protein in the Database

Gamma-aminobutyric acid receptor subunit gamma-2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)