SAXSdb — 6lbi

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

Forkhead box protein O1

Homo sapiens

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain C； UniProt 151–265 Chain D； UniProt 151–265	Not recorded	IRE0 × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；50 mM NaAc, pH 4.7, 12%-18% PEG4000 (w/v), 200 mM NaCl, 10 mM MgCl2 and 1 mM TCEP.	Resolution 3.07 Å R-free 0.264
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain G； UniProt 151–265 Chain H； UniProt 151–265	Not recorded	IRE0 × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；50 mM NaAc, pH 4.7, 12%-18% PEG4000 (w/v), 200 mM NaCl, 10 mM MgCl2 and 1 mM TCEP.	Resolution 3.07 Å R-free 0.264
3	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain K； UniProt 151–265 Chain L； UniProt 151–265	Not recorded	IRE0 × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；50 mM NaAc, pH 4.7, 12%-18% PEG4000 (w/v), 200 mM NaCl, 10 mM MgCl2 and 1 mM TCEP.	Resolution 3.07 Å R-free 0.264

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 6LBI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3CO6 Crystal Structure of FoxO1 DBD Bound to DBE1 DNA Deposited 2008-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 151–249（99 aa）	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；22% PEG 4000, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.256
3CO7 Crystal Structure of FoxO1 DBD Bound to DBE2 DNA Deposited 2008-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 151–266（116 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；21% PEG 4000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.91 Å R-free 0.276
3CO7 Crystal Structure of FoxO1 DBD Bound to DBE2 DNA Deposited 2008-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 151–266（116 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；21% PEG 4000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.91 Å R-free 0.276
3COA Crystal Structure of FoxO1 DBD Bound to IRE DNA Deposited 2008-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 151–266（116 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；30% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.250
3COA Crystal Structure of FoxO1 DBD Bound to IRE DNA Deposited 2008-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 151–266（116 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；30% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.250
4LG0 Structure of a ternary FOXO1-ETS1 DNA complex Deposited 2013-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 143–270（128 aa） Fragment：DNA Binding Domain, UNP residues 143-270	Not recorded	CA CALCIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；30% PEG 400, 0.05M 2-Amino-2-hydroxymethyl-propane-1,3-diol, 0.1M potassium chloride, 0.01M magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.19 Å R-free 0.243
5DUI Identification of a new FoxO1 binding site that precludes CREB binding at the glucose-6-phosphatase catalytic subunit gene promoter Deposited 2015-09-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 151–259（109 aa） Fragment：unp residues 151-259 Chain B 151–259（109 aa） Fragment：unp residues 151-259	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；14-18% PEG 8000 0.1M Ammonium sulfate 20mM Magnesium chloride 50mM MES pH 5.6 10% glycerol	Resolution 2.31 Å R-free 0.245
6QVW Solution structure of the free FOXO1 DNA binding domain Deposited 2019-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 159–272（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 70；Pressure 1 NMR sample composition 380 uM [U-13C; U-15N] FOXO1 DBD, 20 mM sodium phosphate, 50 mM potassium chloride, 2 mM TCEP, 100 % n/a n/a, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6QZR 14-3-3 sigma in complex with FOXO1 pT24 peptide Deposited 2019-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 19–29（11 aa） Chain O 19–29（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Bis-Tris propane pH 7, 0.2M Sodium nitrate, 28% (w/v) PEG400, 5% (w/v) glycerol	Resolution 2.30 Å R-free 0.267
6QZR 14-3-3 sigma in complex with FOXO1 pT24 peptide Deposited 2019-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 19–29（11 aa） Chain P 19–29（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Bis-Tris propane pH 7, 0.2M Sodium nitrate, 28% (w/v) PEG400, 5% (w/v) glycerol	Resolution 2.30 Å R-free 0.267
6QZR 14-3-3 sigma in complex with FOXO1 pT24 peptide Deposited 2019-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain J 19–29（11 aa） Chain U 19–29（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Bis-Tris propane pH 7, 0.2M Sodium nitrate, 28% (w/v) PEG400, 5% (w/v) glycerol	Resolution 2.30 Å R-free 0.267
6QZR 14-3-3 sigma in complex with FOXO1 pT24 peptide Deposited 2019-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 19–29（11 aa） Chain T 19–29（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Bis-Tris propane pH 7, 0.2M Sodium nitrate, 28% (w/v) PEG400, 5% (w/v) glycerol	Resolution 2.30 Å R-free 0.267
8A62 Small molecule stabilizer (compound 2) for FOXO1 and 14-3-3 Deposited 2022-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 20–29（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 4 L7L (3~{S})-1-[3,5-bis(chloranyl)-4-oxidanyl-phenyl]carbonyl-~{N}-[2-[2-(dimethylamino)ethyldisulfanyl]ethyl]piperidine-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.095 M HEPES pH 7.5, 0.19 M CaCl2, 5% glycerol, 24% PEG 400	Resolution 1.60 Å R-free 0.182
8A65 Small molecule stabilizer (compound 3) for FOXO1 and 14-3-3 Deposited 2022-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–28（8 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 4 L70 (3~{S})-1-[2-azanyl-3,5-bis(chloranyl)phenyl]carbonyl-~{N}-[2-[2-(dimethylamino)ethyldisulfanyl]ethyl]piperidine-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.095 M HEPES pH 7.3, 0.19 M CaCl2, 5% glycerol, 25% PEG 400	Resolution 1.60 Å R-free 0.193

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FOXO1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 4–118； UniProt 151–265 Author chain D； PDBConstruct 4–118； UniProt 151–265 Author chain G； PDBConstruct 4–118； UniProt 151–265 Author chain H； PDBConstruct 4–118； UniProt 151–265 Author chain K； PDBConstruct 4–118； UniProt 151–265 Author chain L； PDBConstruct 4–118； UniProt 151–265

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	6lbi
Deposition date deposition_date	2019-11-14
Structure title title	Crystal Structure of FOXO1-DBD homodimer bound to a palindromic DNA sequence
Keywords keywords	Transcription factor, FOXO1, protein-DNA complex, DNA binding, 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	34.18 Å
Radius of gyration Rg (electron density) rg_electron	33.68 Å
Forward intensity I(0) i0	200633000.00
Molecular weight molecular_weight	89441.0 kDa
Excluded volume excluded_volume	101460 Å³
Envelope volume envelope_volume	152860 Å³
Hydration-shell volume shell_volume	38975 Å³
Envelope diameter envelope_diameter	113.6 Å
Shell Rg shell_rg	39.38 Å
Envelope Rg envelope_rg	32.56 Å
Shape Rg shape_rg	33.67 Å
Total Rg total_rg	34.09 Å
Total atoms total_atoms	6172
Residues n_residues	598
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	108.6 Å
Rg (real space) rg_real	34.08 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	2.0060e+08
I(0) uncertainty (real space) i0_real_error	3.6080e+06
Rg (reciprocal space) rg_reciprocal	34.14 Å
I(0) (reciprocal space) i0_reciprocal	200600000.0000
Solution quality estimate total_estimate	0.8939
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.2 Å
Skewness Skewness skewness	0.142
Kurtosis Kurtosis kurtosis	-0.480
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17020000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	IRE0
Molecular weight formula_weight	6133.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,B,E,F,I,J
Atom count atom_count	6172

ACCGTAAACATGTTTACGGT

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Forkhead box protein O1
Molecular weight formula_weight	13220.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,H,K,L

GPSKSSSSRRNAWGNLSYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6lbic_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d6lbid_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d6lbig_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d6lbih_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d6lbik_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d6lbil_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

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8. Citations (1)

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Unit-cell length a length_a	67.732 Å
Unit-cell length b length_b	89.090 Å
Unit-cell length c length_c	194.166 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	24

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

Resolution resolution	3.067 Å
Low-resolution limit resolution_low	46.793 Å
R factor r_factor	0.2286
R_work r_work	0.2267
R_free r_free	0.2641

fit	/app/data/saxs_computation/lb/6lbi/6lbi.fit
pddf	/app/data/pr_computation/lb/6lbi/6lbi.pr.out
profile	/app/data/saxs_computation/lb/6lbi/6lbi.dat

Crystal Structure of FOXO1-DBD homodimer bound to a palindromic DNA sequence

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

Forkhead box protein O1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)