SAXSdb — 13fr

▼

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

START domain-containing protein

Caenorhabditis elegans

UniProt Q19819

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 221–447	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；50 mM sodium cacodylate pH 6.5, 100 mM magnesium acetate, 200 mM potassium chloride, 14% w/v PEG 8000	Resolution 2.09 Å R-free 0.243
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 221–447	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；50 mM sodium cacodylate pH 6.5, 100 mM magnesium acetate, 200 mM potassium chloride, 14% w/v PEG 8000	Resolution 2.09 Å R-free 0.243
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 221–447	Not recorded	CLR CHOLESTEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；50 mM sodium cacodylate pH 6.5, 100 mM magnesium acetate, 200 mM potassium chloride, 14% w/v PEG 8000	Resolution 2.09 Å R-free 0.243
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 221–447	Not recorded	CLR CHOLESTEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；50 mM sodium cacodylate pH 6.5, 100 mM magnesium acetate, 200 mM potassium chloride, 14% w/v PEG 8000	Resolution 2.09 Å R-free 0.243

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 13FR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
13FT START domain of Caenorhabditis elegans StAR-related lipid transfer protein 3 (STARD3) Deposited 2026-05-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 221–447（227 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM sodium citrate tribasic dihydrate pH 5.0, 200 mM lithium sulfate; 22% v/v PEG 200	Resolution 2.01 Å R-free 0.213
13FT START domain of Caenorhabditis elegans StAR-related lipid transfer protein 3 (STARD3) Deposited 2026-05-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 221–447（227 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM sodium citrate tribasic dihydrate pH 5.0, 200 mM lithium sulfate; 22% v/v PEG 200	Resolution 2.01 Å R-free 0.213

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

View Construct and Data Evidence

UniProt name	Q19819_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–228； UniProt 221–447 Author chain B； PDBConstruct 2–228； UniProt 221–447 Author chain C； PDBConstruct 2–228； UniProt 221–447 Author chain D； PDBConstruct 2–228； UniProt 221–447

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	13fr
Deposition date deposition_date	2026-05-04
最后修订 last_revision	2026-05-13
Structure title title	Cholesterol complex of the START domain of Caenorhabditis elegans StAR-related lipid transfer protein 3 (STARD3)
Keywords keywords	cholesterol, cholesterol traffic, cholesterol metabolism, physical biochemistry, STARD3, START domain, NPC1/NPC2, LIPID TRANSPORT; LIPID TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	32.82 Å
Radius of gyration Rg (electron density) rg_electron	32.06 Å
Forward intensity I(0) i0	149970000.00
Molecular weight molecular_weight	99428.0 kDa
Excluded volume excluded_volume	125200 Å³
Envelope volume envelope_volume	160200 Å³
Hydration-shell volume shell_volume	41092 Å³
Envelope diameter envelope_diameter	110.1 Å
Shell Rg shell_rg	39.46 Å
Envelope Rg envelope_rg	31.77 Å
Shape Rg shape_rg	32.03 Å
Total Rg total_rg	32.77 Å
Total atoms total_atoms	7001
Residues n_residues	851
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

▼

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

Maximum dimension Dmax dmax	104.3 Å
Rg (real space) rg_real	32.70 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	1.5000e+08
I(0) uncertainty (real space) i0_real_error	2.2580e+06
Rg (reciprocal space) rg_reciprocal	32.76 Å
I(0) (reciprocal space) i0_reciprocal	150000000.0000
Solution quality estimate total_estimate	0.9054
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.3 Å
Skewness Skewness skewness	0.179
Kurtosis Kurtosis kurtosis	-0.593
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51400000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.945

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	START domain-containing protein
Molecular weight formula_weight	26256.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7417

GAEFSSDEEARSRLLVPPDTKRLFEITLRECLDQVEELMRDSRLGGWKTLRSANPTVLQGPDNYFLVRSEFNKFPALVLFNIAWKDMLKWNTQVIEGKMIAHLDNATDLYYSVSAPAMRGYISSRDFLDLRKIKLDSSADVYTGYFVSVESNLCPNNGNPKIVRGHNFPSMIRTLKDEAGVTYFEWLMKTDLKGGLPRRLVHSGMVNYFSEHVKRMNEFAETHYHCPP

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI Class编号 ncbi_taxonomy_id	6239
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	401

▶

8. Citations (1)

▶

Unit-cell length a length_a	84.512 Å
Unit-cell length b length_b	77.667 Å
Unit-cell length c length_c	85.294 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	29.370 Å
R factor r_factor	0.2119
R_work r_work	0.2102
R_free r_free	0.2431

fit	/app/data/saxs_computation/3f/13fr/13fr.fit
pddf	/app/data/pr_computation/3f/13fr/13fr.pr.out
profile	/app/data/saxs_computation/3f/13fr/13fr.dat

Cholesterol complex of the START domain of Caenorhabditis elegans StAR-related lipid transfer protein 3 (STARD3)

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

START domain-containing protein

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