SAXSdb — 1osv

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

Bile acid receptor

Rattus norvegicus

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 241–469	Fragment：ligand binding domain (FXR-LBD)	Nuclear receptor coactivator 2 × 1 （Q61026） CHC 6-ETHYL-CHENODEOXYCHOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；283 K；PEG 8000,Ethylene Glycol, PIPES , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.50 Å R-free 0.276
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 241–469	Fragment：ligand binding domain (FXR-LBD)	Nuclear receptor coactivator 2 × 2 （Q61026） CHC 6-ETHYL-CHENODEOXYCHOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；283 K；PEG 8000,Ethylene Glycol, PIPES , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.50 Å R-free 0.276

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 1OSV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OT7 Structural Basis for 3-deoxy-CDCA Binding and Activation of FXR Deposited 2003-03-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 240–468（229 aa） Fragment：ligand binding domain	Not recorded	CHC 6-ETHYL-CHENODEOXYCHOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；282 K；PEG 8000, Ethylene glycol, PIPES, Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 282K	Resolution 2.90 Å R-free 0.279
1OT7 Structural Basis for 3-deoxy-CDCA Binding and Activation of FXR Deposited 2003-03-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 240–468（229 aa） Fragment：ligand binding domain	Not recorded	IU5 ISO-URSODEOXYCHOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；282 K；PEG 8000, Ethylene glycol, PIPES, Ammonium Sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 282K	Resolution 2.90 Å R-free 0.279

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

View Construct and Data Evidence

UniProt name	NR1H4_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–230； UniProt 241–469 Author chain B； PDBConstruct 2–230； UniProt 241–469

Nuclear receptor coactivator 2

OrganismNot specified

UniProt Q61026

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 741–752	Fragment：Residues (741-752)	Bile acid receptor × 1 （Q62735） CHC 6-ETHYL-CHENODEOXYCHOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；283 K；PEG 8000,Ethylene Glycol, PIPES , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.50 Å R-free 0.276
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 741–752 Chain E； UniProt 741–752	Fragment：Residues (741-752)	Bile acid receptor × 1 （Q62735） CHC 6-ETHYL-CHENODEOXYCHOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；283 K；PEG 8000,Ethylene Glycol, PIPES , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.50 Å R-free 0.276

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 1OSV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L2I Human Estrogen Receptor alpha Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol and a Glucocorticoid Receptor Interacting Protein 1 NR box II Peptide Deposited 2002-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 686–698（13 aa） Fragment：NR box II (residues 686-698) Chain D 686–698（13 aa） Fragment：NR box II (residues 686-698)	Not recorded	CL CHLORIDE ION × 1 ETC (R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；16% (w/v) PEG 4000, 50 mM Magnesium chloride, 53 mM Tris pH 8.8 292-294 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.243
1L2I Human Estrogen Receptor alpha Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol and a Glucocorticoid Receptor Interacting Protein 1 NR box II Peptide Deposited 2002-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 686–698（13 aa） Fragment：NR box II (residues 686-698) Chain D 686–698（13 aa） Fragment：NR box II (residues 686-698)	Not recorded	CL CHLORIDE ION × 1 ETC (R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；16% (w/v) PEG 4000, 50 mM Magnesium chloride, 53 mM Tris pH 8.8 292-294 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.243
1WM0 PPARgamma in complex with a 2-BABA compound Deposited 2004-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 684–697（14 aa）	Not recorded	PLB 2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG3000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.295
3MNE Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by F608S mutation at 1.96A Deposited 2010-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 740–752（13 aa） Fragment：TIF2 coactivator motif, residues 740-752	Not recorded	GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；0.5 M ammonium sulfate, 0.9 M sodium tartrate, 0.1 M PIPES pH 7.0, VAPOR DIFFUSION, SITTING DROP	Resolution 1.96 Å R-free 0.185
3MNO Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, F608S) mutations at 1.55A Deposited 2010-04-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 740–752（13 aa） Fragment：TIF2 coactivator motif, residues 740-752	Not recorded	GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1 SCN THIOCYANATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；0.2 M sodium thiocyanate, 0.1 M Bis-Tris pH 6.5, 0.7 M lithium sulfate, 10 % Glycerol, VAPOR DIFFUSION, HANGING DROP	Resolution 1.55 Å R-free 0.187
3MNP Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, V708A, E711G) mutations at 1.50A Deposited 2010-04-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 740–752（13 aa） Fragment：TIF2 coactivator motif, residues 740-752	Not recorded	GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1 SCN THIOCYANATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；0.1 M Tris pH 8.5, 0.1 M sodium thiocyanate, 9 % PEG 10000, VAPOR DIFFUSION, SITTING DROP	Resolution 1.50 Å R-free 0.201

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCOA2_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–12； UniProt 741–752 Author chain D； PDBConstruct 1–12； UniProt 741–752 Author chain E； PDBConstruct 1–12； UniProt 741–752

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	1osv
Deposition date deposition_date	2003-03-20
Structure title title	STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCLEAR RECEPTOR FXR
Keywords keywords	LBD, bile acid, coactivator, nuclear receptor, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	25.73 Å
Radius of gyration Rg (electron density) rg_electron	24.78 Å
Forward intensity I(0) i0	52349300.00
Molecular weight molecular_weight	58462.0 kDa
Excluded volume excluded_volume	74184 Å³
Envelope volume envelope_volume	88693 Å³
Hydration-shell volume shell_volume	29920 Å³
Envelope diameter envelope_diameter	90.5 Å
Shell Rg shell_rg	32.09 Å
Envelope Rg envelope_rg	24.87 Å
Shape Rg shape_rg	24.78 Å
Total Rg total_rg	25.62 Å
Total atoms total_atoms	4113
Residues n_residues	494
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

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

Maximum dimension Dmax dmax	94.9 Å
Rg (real space) rg_real	27.03 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	5.2620e+07
I(0) uncertainty (real space) i0_real_error	7.9340e+05
Rg (reciprocal space) rg_reciprocal	25.73 Å
I(0) (reciprocal space) i0_reciprocal	52350000.0000
Solution quality estimate total_estimate	0.6368
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.624
Kurtosis Kurtosis kurtosis	0.256
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	3.6070
Highest regularization parameter α highest_alpha	16660000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.664; Stabil: 0.871; Sysdev: 0.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.769

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Bile acid receptor
Molecular weight formula_weight	26850.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4265

AELTVDQQTLLDYIMDSYSKQRMPQEITNKILKEEFSAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPAGHADLLEERIRKSGISDEYITPMFSFYKSVGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIYQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Nuclear receptor coactivator 2
Molecular weight formula_weight	1464.7 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E

ENALLRYLLDKD

Entity 3 Entity 3 non-polymer

Description description	6-ETHYL-CHENODEOXYCHOLIC ACID
Molecular weight formula_weight	420.6 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	152

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1osva1
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	d1osva2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1osvb1
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	d1osvb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1osvA00
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	1osvB00
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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8. Citations (1)

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Unit-cell length a length_a	98.970 Å
Unit-cell length b length_b	108.518 Å
Unit-cell length c length_c	69.464 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.880 Å
R factor r_factor	0.2420
R_work r_work	0.2420
R_free r_free	0.2760

fit	/app/data/saxs_computation/os/1osv/1osv.fit
pddf	/app/data/pr_computation/os/1osv/1osv.pr.out
profile	/app/data/saxs_computation/os/1osv/1osv.dat

STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCLEAR RECEPTOR FXR

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

Bile acid receptor

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear receptor coactivator 2

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)