2nxx

Crystal Structure of the Ligand-Binding Domains of the T.castaneum (Coleoptera) Heterodimer EcrUSP Bound to Ponasterone A

Method: X-RAY DIFFRACTION

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

Ultraspiracle (USP, NR2B4)

Tribolium castaneum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ecdysone Receptor (EcR, NRH1) × 1 （A1JUG3） 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ecdysone Receptor (EcR, NRH1) × 1 （A1JUG3） 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ecdysone Receptor (EcR, NRH1) × 1 （A1JUG3） 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ecdysone Receptor (EcR, NRH1) × 1 （A1JUG3） 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A1JUG2_TRICA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–235； UniProt 174–407 Author chain B； PDBConstruct 2–235； UniProt 174–407 Author chain C； PDBConstruct 2–235； UniProt 174–407 Author chain D； PDBConstruct 2–235； UniProt 174–407

Ecdysone Receptor (EcR, NRH1)

Tribolium castaneum

UniProt A1JUG3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ultraspiracle (USP, NR2B4) × 1 （A1JUG2） 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ultraspiracle (USP, NR2B4) × 1 （A1JUG2） 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ultraspiracle (USP, NR2B4) × 1 （A1JUG2） 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ultraspiracle (USP, NR2B4) × 1 （A1JUG2） 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A1JUG3_TRICA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 5–248； UniProt 306–549 Author chain F； PDBConstruct 5–248； UniProt 306–549 Author chain G； PDBConstruct 5–248； UniProt 306–549 Author chain H； PDBConstruct 5–248； UniProt 306–549

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	2nxx
Deposition date deposition_date	2006-11-20
Structure title title	Crystal Structure of the Ligand-Binding Domains of the T.castaneum (Coleoptera) Heterodimer EcrUSP Bound to Ponasterone A
Keywords keywords	Hormone Receptor, apo and holo Ligand Binding Pocket, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
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.

2nxx__assembly_1__model_1

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

Download this curve (.dat)

2nxx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nxx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.42 Å
Rg (electron density)	23.18 Å
Total Rg	23.99 Å
Atom count	3735
Residues	458
Excluded volume	67300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nxx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nxx__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2nxx__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2nxx__assembly_4__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	Ultraspiracle (USP, NR2B4)
Molecular weight formula_weight	26576.9 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	15241

MTSNLQADMPLERIIEAEKRVECNDPLVALVVNENNTTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVLATGLTVNKSTAHAVGVGNIYDRVLSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDVPIDTFLMEMLEGTTDS

Source Source

Source organism organism	Tribolium castaneum
Common name common_name	red flour beetle
NCBI taxonomy ID ncbi_taxonomy_id	7070
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ecdysone Receptor (EcR, NRH1)
Molecular weight formula_weight	28879.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

GSHMNGSKGISPEQEELIHRLVYFQNEYEHPSEEDVKRIINQPMDGEDQCDVRFRHITEITILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQTDSILFVNNQPYSRDSYNLAGMGETIEDLLHFCRTMYSMRVDNAEYALLTAIVIFSERPALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAKLLSVLTELRTLGNQNSEMCFSLKLKNKKLPPFLAEIWDVDLKT

Source Source

Source organism organism	Tribolium castaneum
Common name common_name	red flour beetle
NCBI taxonomy ID ncbi_taxonomy_id	7070
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE
Molecular weight formula_weight	464.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2nxxa_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

Domain ID domain_id	d2nxxb_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

Domain ID domain_id	d2nxxc_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

Domain ID domain_id	d2nxxd_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

Domain ID domain_id	d2nxxe_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

Domain ID domain_id	d2nxxf_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

Domain ID domain_id	d2nxxg_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

Domain ID domain_id	d2nxxh_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (8 domains)

Domain ID domain_id	2nxxA00
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	2nxxB00
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	2nxxC00
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	2nxxD00
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	2nxxE00
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	2nxxF00
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	2nxxG00
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	2nxxH00
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	77.540 Å
Unit-cell length b length_b	89.628 Å
Unit-cell length c length_c	160.247 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.97 °
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	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2490
R_work r_work	0.2490
R_free r_free	0.2810

Crystal Structure of the Ligand-Binding Domains of the T.castaneum (Coleoptera) Heterodimer EcrUSP Bound to Ponasterone A

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

Ultraspiracle (USP, NR2B4)

State in the Current Structure

Other States of the Same Protein in the Database

Ecdysone Receptor (EcR, NRH1)

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

2nxx__assembly_1__model_1

2nxx__assembly_1__model_1 | I(q)

2nxx__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of the Ligand-Binding Domains of the T.castaneum (Coleoptera) Heterodimer EcrUSP Bound to Ponasterone A

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

Ultraspiracle (USP, NR2B4)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ecdysone Receptor (EcR, NRH1)

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

2nxx__assembly_1__model_1

2nxx__assembly_1__model_1 | I(q)

2nxx__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)