SAXSdb — 3gyt

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

Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily

Strongyloides stercoralis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SRC1 × 1 (14beta,17alpha,25R)-3-oxocholest-4-en-26-oic acid × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9XZJ5_9BILA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–244； UniProt 512–753

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	3gyt
Deposition date deposition_date	2009-04-05
Structure title title	Nuclear receptor DAF-12 from parasitic nematode Strongyloides stercoralis in complex with its physiological ligand dafachronic acid delta 4
Keywords keywords	;nuclear receptor, ligand binding domain, dafachronic acid, SRC1, nematode, Strongyloides stercoralis, DNA-binding, Metal-binding, Nucleus, Receptor, Transcription, Transcription regulation, Zinc, Zinc-finger ;; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3gyt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3gyt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gyt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.58 Å
Rg (electron density)	18.14 Å
Total Rg	19.08 Å
Atom count	2052
Residues	252
Excluded volume	36897 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gyt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily
Molecular weight formula_weight	27797.9 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	2220

GSYTLSEKDLKELDSIRDSFQCMNEPLDNDQQASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMFDKLRPDIKDTQKKGFLHFFNLLHSDVRKNDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVTLFLGAGNTTEAASLPKEFFATNY

Source Source

Source organism organism	Strongyloides stercoralis
NCBI taxonomy ID ncbi_taxonomy_id	6248
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SRC1
Molecular weight formula_weight	1500.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AQQKSLLQQLLTE

Entity 3 Entity 3 non-polymer

Description description	(14beta,17alpha,25R)-3-oxocholest-4-en-26-oic acid
Molecular weight formula_weight	414.6 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	168

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3gytA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

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Unit-cell length a length_a	118.947 Å
Unit-cell length b length_b	118.947 Å
Unit-cell length c length_c	40.225 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1950
R_work r_work	0.1920
R_free r_free	0.2320

Nuclear receptor DAF-12 from parasitic nematode Strongyloides stercoralis in complex with its physiological ligand dafachronic acid delta 4

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

Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3gyt__assembly_1__model_1

3gyt__assembly_1__model_1 | I(q)

3gyt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Nuclear receptor DAF-12 from parasitic nematode Strongyloides stercoralis in complex with its physiological ligand dafachronic acid delta 4

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

Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3gyt__assembly_1__model_1

3gyt__assembly_1__model_1 | I(q)

3gyt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)