SAXSdb — 5gv2

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

GATS-like protein 3

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–329 Chain C； UniProt 1–329	Not recorded	MG MAGNESIUM ION × 1 ARG ARGININE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；287 K；PEG 3350, Magnesium acetate tetrahydrate	Resolution 2.06 Å R-free 0.238

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 5GV2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5GS9 Crystal structure of CASTOR1-arginine Deposited 2016-08-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–329（329 aa） Chain B 1–329（329 aa）	Not recorded	ARG ARGININE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.1M sodium citrate (pH 5.0), 20% (w/v) PEG 8000	Resolution 2.50 Å R-free 0.224
5GS9 Crystal structure of CASTOR1-arginine Deposited 2016-08-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–329（329 aa） Chain D 1–329（329 aa）	Not recorded	ARG ARGININE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.1M sodium citrate (pH 5.0), 20% (w/v) PEG 8000	Resolution 2.50 Å R-free 0.224
5GT7 Crystal Structure of Arg-bound CASTOR1 Deposited 2016-08-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa）	Not recorded	ARG ARGININE × 2 MLI MALONATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；5 % (w/v) PEG3350, 0.1 M Na Malonate pH 5.0	Resolution 2.05 Å R-free 0.211
5GT7 Crystal Structure of Arg-bound CASTOR1 Deposited 2016-08-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–323（323 aa） Chain D 1–323（323 aa）	Not recorded	ARG ARGININE × 2 MLI MALONATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；5 % (w/v) PEG3350, 0.1 M Na Malonate pH 5.0	Resolution 2.05 Å R-free 0.211
5GT8 Crystal Structure of apo-CASTOR1 Deposited 2016-08-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–329（329 aa） Chain C 1–329（329 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；21%(w/v) PEG3350, 0.1M Tris pH 5.0, 0.2M MgCl2, 0.2% n- dodecyl- N, N- dimethylamine-N-oxide	Resolution 2.80 Å R-free 0.265
5GT8 Crystal Structure of apo-CASTOR1 Deposited 2016-08-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–329（329 aa） Chain D 1–329（329 aa） Fragment：UNP residues A285I	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；21%(w/v) PEG3350, 0.1M Tris pH 5.0, 0.2M MgCl2, 0.2% n- dodecyl- N, N- dimethylamine-N-oxide	Resolution 2.80 Å R-free 0.265
5I2C Arginine-bound CASTOR1 from Homo sapiens Deposited 2016-02-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–329（329 aa） Chain B 1–329（329 aa）	Not recorded	ARG ARGININE × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291.15 K；0.1 M sodium acetate, 0.25 M ammonium acetate, 22.5% PEG 3350	Resolution 1.80 Å R-free 0.204
5I2C Arginine-bound CASTOR1 from Homo sapiens Deposited 2016-02-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–329（329 aa） Chain D 1–329（329 aa）	Not recorded	ARG ARGININE × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291.15 K；0.1 M sodium acetate, 0.25 M ammonium acetate, 22.5% PEG 3350	Resolution 1.80 Å R-free 0.204
9DX2 Human GATOR2 complex - CASTOR1 bound state Deposited 2024-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–328（328 aa） Chain F 1–328（328 aa） Chain G 1–328（328 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9KP4 Crystal structure of human CASTOR1 in apo form Deposited 2024-11-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–329（329 aa） Chain B 1–329（329 aa）	Not recorded	NH4 AMMONIUM ION × 2 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Barium chloride, 30% v/v ethanol, 0.2 M NH4Ac, 0.1 M Tris pH 8.5, and 25% PEG 3350.	Resolution 3.08 Å R-free 0.264
9KP4 Crystal structure of human CASTOR1 in apo form Deposited 2024-11-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–329（329 aa） Chain D 1–329（329 aa）	Not recorded	NH4 AMMONIUM ION × 2 ACY ACETIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Barium chloride, 30% v/v ethanol, 0.2 M NH4Ac, 0.1 M Tris pH 8.5, and 25% PEG 3350.	Resolution 3.08 Å R-free 0.264
9LVK Cryo-EM structure of CASTOR1 bound human GATOR2 complex Deposited 2025-02-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain U 1–329（329 aa） Chain V 1–329（329 aa）	Mutation：D304A Mutation：D304A	ZN ZINC ION × 31	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 Å
9LWF Cryo-EM structure of dual sensor bound GATOR2 complex Deposited 2025-02-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain U 1–329（329 aa） Chain V 1–329（329 aa）	Mutation：D304A Mutation：D304A	ZN ZINC ION × 32	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
9OTI GATOR2 complex bound to arginine sensor CASTOR1 Deposited 2025-05-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain U 1–329（329 aa） Chain V 1–329（329 aa）	Mutation：D304A, S111A Mutation：D304A, S111A	ZN ZINC ION × 29	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GATL3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–348； UniProt 1–329 Author chain C； PDBConstruct 20–348； UniProt 1–329

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	5gv2
Deposition date deposition_date	2016-09-01
Structure title title	Crystal structure of Arginine-bound CASTOR1 from Homo sapiens
Keywords keywords	CASTOR1, Arginine, Dimer, SIGNALING PROTEIN; SIGNALING PROTEIN
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	31.63 Å
Radius of gyration Rg (electron density) rg_electron	30.66 Å
Forward intensity I(0) i0	69032200.00
Molecular weight molecular_weight	68068.0 kDa
Excluded volume excluded_volume	86248 Å³
Envelope volume envelope_volume	108250 Å³
Hydration-shell volume shell_volume	30986 Å³
Envelope diameter envelope_diameter	109.5 Å
Shell Rg shell_rg	35.89 Å
Envelope Rg envelope_rg	31.10 Å
Shape Rg shape_rg	30.64 Å
Total Rg total_rg	31.23 Å
Total atoms total_atoms	4806
Residues n_residues	611
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	104.5 Å
Rg (real space) rg_real	31.93 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	6.9030e+07
I(0) uncertainty (real space) i0_real_error	1.0760e+06
Rg (reciprocal space) rg_reciprocal	31.81 Å
I(0) (reciprocal space) i0_reciprocal	69030000.0000
Solution quality estimate total_estimate	0.8251
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.3 Å
Skewness Skewness skewness	0.497
Kurtosis Kurtosis kurtosis	-0.534
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	36390000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.707; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.838; Smooth: 0.762

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	GATS-like protein 3
Molecular weight formula_weight	38550.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A
Atom count atom_count	4955

MGSHHHHHHSSGLVPRGSHMELHILEHRVRVLSVARPGLWLYTHPLIKLLFLPRRSRCKFFSLTETPEDYTLMVDEEGFKELPPSEFLQVAEATWLVLNVSSHSGAAVQAAGVTKIARSVIAPLAEHHVSVLMLSTYQTDFILVREQDLSVVIHTLAQEFDIYREVGGEPVPVTRDDSSNGFPRTQHGPSPTVHPIQSPQNRFCVLTLDPETLPAIATTLIDVLFYSHSTPKEAASSSPEPSSITFFAFSLIEGYISIVMDAETQKKFPSDLLLTSSSGELWRMVRIGGQPLGFDECGIVAQIAGPLAAADISAYYISTFNFDHALVPEDGIGSVIEVLQRRQEGLASR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5gv2A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2130 — VC0802-like
Homologous superfamily homologous superfamily	10 — VC0802-like

Domain ID domain_id	5gv2C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2130 — VC0802-like
Homologous superfamily homologous superfamily	10 — VC0802-like

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8. Citations (1)

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Unit-cell length a length_a	47.547 Å
Unit-cell length b length_b	76.834 Å
Unit-cell length c length_c	95.223 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.060 Å
Low-resolution limit resolution_low	94.660 Å
R factor r_factor	0.1925
R_work r_work	0.1900
R_free r_free	0.2383

fit	/app/data/saxs_computation/gv/5gv2/5gv2.fit
pddf	/app/data/pr_computation/gv/5gv2/5gv2.pr.out
profile	/app/data/saxs_computation/gv/5gv2/5gv2.dat

Crystal structure of Arginine-bound CASTOR1 from Homo sapiens

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

GATS-like protein 3

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