3dzy

Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with Rosiglitazone, 9-cis Retinoic Acid and NCOA2 Peptide

Method: X-RAY DIFFRACTION

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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–DNA	Heteromer	Protein 4 DNA 2	Peroxisome proliferator-activated receptor gamma × 1 （P37231） ;DNA (5'-D(DCPDAPDAPDAPDCPDTPDAPDGPDGPDTPDCPDAPDAPDAPDGPDGPDTPDCPDAPDG)-3') ; × 1 ;DNA (5'-D(DCPDTPDGPDAPDCPDCPDTPDTPDTPDGPDAPDCPDCPDTPDAPDGPDTPDTPDTPDG)-3') ; × 1 NCOA2 Peptide × 2 （Q15596） (9cis)-retinoic acid × 1 ZINC ION × 4 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) × 1	Consistent with all polymers

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 16–467； UniProt 11–462

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–DNA	Heteromer	Protein 4 DNA 2	Retinoic acid receptor RXR-alpha × 1 （P19793） ;DNA (5'-D(DCPDAPDAPDAPDCPDTPDAPDGPDGPDTPDCPDAPDAPDAPDGPDGPDTPDCPDAPDG)-3') ; × 1 ;DNA (5'-D(DCPDTPDGPDAPDCPDCPDTPDTPDTPDGPDAPDCPDCPDTPDAPDGPDTPDTPDTPDG)-3') ; × 1 NCOA2 Peptide × 2 （Q15596） (9cis)-retinoic acid × 1 ZINC ION × 4 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) × 1	Consistent with all polymers

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 16–419； UniProt 102–505

NCOA2 Peptide

OrganismNot specified

UniProt Q15596

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	Retinoic acid receptor RXR-alpha × 1 （P19793） Peroxisome proliferator-activated receptor gamma × 1 （P37231） ;DNA (5'-D(DCPDAPDAPDAPDCPDTPDAPDGPDGPDTPDCPDAPDAPDAPDGPDGPDTPDCPDAPDG)-3') ; × 1 ;DNA (5'-D(DCPDTPDGPDAPDCPDCPDTPDTPDTPDGPDAPDCPDCPDTPDAPDGPDTPDTPDTPDG)-3') ; × 1 (9cis)-retinoic acid × 1 ZINC ION × 4 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCOA2_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–13； UniProt 685–697 Author chain G； PDBConstruct 1–13； UniProt 685–697

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	3dzy
Deposition date deposition_date	2008-07-30
Structure title title	Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with Rosiglitazone, 9-cis Retinoic Acid and NCOA2 Peptide
Keywords keywords	;DNA-binding, Host-virus interaction, Metal-binding, Nucleus, Receptor, Transcription, Transcription regulation, Zinc-finger, Activator, Diabetes mellitus, Disease mutation, Obesity, Phosphoprotein, Transcription-DNA COMPLEX ;; Transcription/DNA
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.

3dzy__assembly_1__model_1

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

Download this curve (.dat)

3dzy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dzy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.06 Å
Rg (electron density)	29.68 Å
Total Rg	30.45 Å
Atom count	6271
Residues	715
Excluded volume	109980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dzy__assembly_1__model_1`	hexameric （6）	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 (8)

Entity 1 Entity 1 polymer

Description description	Retinoic acid receptor RXR-alpha
Molecular weight formula_weight	51527.9 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	6271

MAHHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQMT

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	48163.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAHHHHHHVDDDDKMYQSAIKVEPASPPYYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCDLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

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	;DNA (5'-D(DCPDAPDAPDAPDCPDTPDAPDGPDGPDTPDCPDAPDAPDAPDGPDGPDTPDCPDAPDG)-3') ;
Molecular weight formula_weight	6176.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CAAACTAGGTCAAAGGTCAG

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(DCPDTPDGPDAPDCPDCPDTPDTPDTPDGPDAPDCPDCPDTPDAPDGPDTPDTPDTPDG)-3') ;
Molecular weight formula_weight	6090.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CTGACCTTTGACCTAGTTTG

Entity 5 Entity 5 polymer

Description description	NCOA2 Peptide
Molecular weight formula_weight	1621.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

EKHKILHRLLQDS

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 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

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3dzyA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	3dzyA02
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	3dzyD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	3dzyD02
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	63.803 Å
Unit-cell length b length_b	146.514 Å
Unit-cell length c length_c	67.223 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.59 °
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	3.100 Å
Low-resolution limit resolution_low	46.710 Å
R factor r_factor	—
R_work r_work	0.2130
R_free r_free	0.2680

Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with Rosiglitazone, 9-cis Retinoic Acid and NCOA2 Peptide

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

NCOA2 Peptide

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

3dzy__assembly_1__model_1

3dzy__assembly_1__model_1 | I(q)

3dzy__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 (8)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with Rosiglitazone, 9-cis Retinoic Acid and NCOA2 Peptide

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

NCOA2 Peptide

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

3dzy__assembly_1__model_1

3dzy__assembly_1__model_1 | I(q)

3dzy__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 (8)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)