SAXSdb — 7fb5

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

Gamma-aminobutyric acid receptor-associated protein

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–117	Not recorded	Reticulophagy regulator 1 × 1 （Q9H6L5）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；containing 0.1 M bis-tris propane pH 8.0, 2.2 M DL-Malic acid	Resolution 2.84 Å R-free 0.244

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 7FB5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YIR Crystal Structure of AnkB LIR/GABARAP 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 D 1–117（117 aa）	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)	Resolution 2.75 Å R-free 0.224
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–117（117 aa）	Not recorded	NI NICKEL (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)	Resolution 2.75 Å R-free 0.224
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–117（117 aa）	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)	Resolution 2.75 Å R-free 0.224
6A9X Crystal Structure of AnkG/GABARAP Complex Deposited 2018-07-16	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；289 K；2.0 M ammonium citrate tribasic, 0.1 M BIS-TRIS propane buffer	Resolution 2.20 Å R-free 0.249

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GBRAP_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 1–117

Reticulophagy regulator 1

OrganismNot specified

UniProt Q9H6L5

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 451–476	Not recorded	Gamma-aminobutyric acid receptor-associated protein × 1 （Q9DCD6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；containing 0.1 M bis-tris propane pH 8.0, 2.2 M DL-Malic acid	Resolution 2.84 Å R-free 0.244

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 7FB5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7BRQ Crystal structure of human FAM134B LIR fused to human GABARAP Deposited 2020-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 450–468（19 aa）	Mutation：F3S,V4T	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；1.91 M ammonium sulfate, 0.1 M sodium citrate pH 5.5, 0.18 M potassium sodium tartrate	Resolution 1.40 Å R-free 0.206

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

View Construct and Data Evidence

UniProt name	RETR1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–26； UniProt 451–476

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	7fb5
Deposition date deposition_date	2021-07-08
Structure title title	Crystal structure of FAM134B/GABARAP complex
Keywords keywords	MEMBRANE PROTEIN, ENDOPLASMIC RETICULUM, AUTOPHAGY, 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	16.35 Å
Radius of gyration Rg (electron density) rg_electron	14.89 Å
Forward intensity I(0) i0	4708860.00
Molecular weight molecular_weight	16111.0 kDa
Excluded volume excluded_volume	20385 Å³
Envelope volume envelope_volume	23111 Å³
Hydration-shell volume shell_volume	13267 Å³
Envelope diameter envelope_diameter	51.5 Å
Shell Rg shell_rg	20.63 Å
Envelope Rg envelope_rg	15.29 Å
Shape Rg shape_rg	14.86 Å
Total Rg total_rg	16.11 Å
Total atoms total_atoms	1142
Residues n_residues	138
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	52.8 Å
Rg (real space) rg_real	16.26 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	4.7090e+06
I(0) uncertainty (real space) i0_real_error	5.7620e+04
Rg (reciprocal space) rg_reciprocal	16.27 Å
I(0) (reciprocal space) i0_reciprocal	4709000.0000
Solution quality estimate total_estimate	0.8878
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	908200.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Gamma-aminobutyric acid receptor-associated protein
Molecular weight formula_weight	13942.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1142

MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL

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	Reticulophagy regulator 1
Molecular weight formula_weight	2967.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EGDDFELLDQSELDQIESELGLTQDQ

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7fb5A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	73.250 Å
Unit-cell length b length_b	73.250 Å
Unit-cell length c length_c	80.852 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.840 Å
Low-resolution limit resolution_low	24.950 Å
R factor r_factor	0.1892
R_work r_work	0.1860
R_free r_free	0.2438

fit	/app/data/saxs_computation/fb/7fb5/7fb5.fit
pddf	/app/data/pr_computation/fb/7fb5/7fb5.pr.out
profile	/app/data/saxs_computation/fb/7fb5/7fb5.dat

Crystal structure of FAM134B/GABARAP complex

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

Gamma-aminobutyric acid receptor-associated protein

State in the Current Structure

Other States of the Same Protein in the Database

Reticulophagy regulator 1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)