SAXSdb — 5ji0

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

Retinoic acid receptor RXR-alpha

Homo sapiens

UniProt P19793

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Peroxisome proliferator-activated receptor gamma × 1 （P37231） Nuclear receptor coactivator 1 × 2 （Q15788） (9cis)-retinoic acid × 1 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Nuclear receptor coactivator 1 × 1 （Q15788） (9cis)-retinoic acid × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RXRA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–242； UniProt 223–462

Peroxisome proliferator-activated receptor gamma

Homo sapiens

UniProt P37231

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Retinoic acid receptor RXR-alpha × 1 （P19793） Nuclear receptor coactivator 1 × 2 （Q15788） (9cis)-retinoic acid × 1 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Nuclear receptor coactivator 1 × 1 （Q15788） 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPARG_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 2–273； UniProt 234–505

Nuclear receptor coactivator 1

OrganismNot specified

UniProt Q15788

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Retinoic acid receptor RXR-alpha × 1 （P19793） Peroxisome proliferator-activated receptor gamma × 1 （P37231） (9cis)-retinoic acid × 1 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Retinoic acid receptor RXR-alpha × 1 （P19793） (9cis)-retinoic acid × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Peroxisome proliferator-activated receptor gamma × 1 （P37231） 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCOA1_HUMAN
Isoform	Q15788-2
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 2–26； UniProt 676–700 Author chain F； PDBConstruct 2–26； UniProt 676–700

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	5ji0
Deposition date deposition_date	2016-04-21
Structure title title	PPARgamma-RXRalpha(S427F) heterodimer in complex with SRC-1, rosiglitazone, and 9-cis-retanoic acid
Keywords keywords	;PPARG, RXRa, SRC1, agonist, nuclear hormone receptor, heterodimer, bladder cancer, muscle invasive bladder cancer, MIBC, TRANSFERASE ;; TRANSFERASE
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.

5ji0__assembly_1__model_1

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

Download this curve (.dat)

5ji0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ji0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.04 Å
Rg (electron density)	23.72 Å
Total Rg	24.67 Å
Atom count	4134
Residues	513
Excluded volume	74762 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ji0__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ji0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ji0__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	Retinoic acid receptor RXR-alpha
Molecular weight formula_weight	27104.4 kDa
Mutation mutation	S427F
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	4370

GMTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRFIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQMT

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peroxisome proliferator-activated receptor gamma
Molecular weight formula_weight	31151.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nuclear receptor coactivator 1
Molecular weight formula_weight	2830.2 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

XCPSSHSSLTERHKILHRLLQEGSPSX

Entity 4 Entity 4 non-polymer

Description description	(9cis)-retinoic acid
Molecular weight formula_weight	300.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
Molecular weight formula_weight	357.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ji0A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	5ji0D00
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	53.880 Å
Unit-cell length b length_b	66.527 Å
Unit-cell length c length_c	165.927 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	45.200 Å
R factor r_factor	0.1948
R_work r_work	0.1921
R_free r_free	0.2460

PPARgamma-RXRalpha(S427F) heterodimer in complex with SRC-1, rosiglitazone, and 9-cis-retanoic acid

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

Retinoic acid receptor RXR-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Peroxisome proliferator-activated receptor gamma

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear receptor coactivator 1

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

5ji0__assembly_1__model_1

5ji0__assembly_1__model_1 | I(q)

5ji0__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

PPARgamma-RXRalpha(S427F) heterodimer in complex with SRC-1, rosiglitazone, and 9-cis-retanoic acid

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

Retinoic acid receptor RXR-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peroxisome proliferator-activated receptor gamma

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nuclear receptor coactivator 1

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

5ji0__assembly_1__model_1

5ji0__assembly_1__model_1 | I(q)

5ji0__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)