SAXSdb — 4wk8

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

Forkhead box protein P3

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 F； UniProt 336–417 Chain G； UniProt 336–417	Fragment：UNP residues 336-417	;DNA (5'-D(TPTPAPGPGPAPAPAPAPTPTPTPGPTPTPTPCPAPTPAPG)-3') ; × 1 ;DNA (5'-D(APAPCPTPAPTPGPAPAPAPCPAPAPAPTPTPTPTPCPCPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；PEG 8000	Resolution 3.40 Å R-free 0.253

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 4WK8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QRF Structure of a domain-swapped FOXP3 dimer Deposited 2011-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain F 336–417（82 aa） Fragment：human FOXP3 DNA Binding Domain Chain G 336–417（82 aa） Fragment：human FOXP3 DNA Binding Domain	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.63；291 K；5 mM HEPES, pH 7.63, 2 mM dithiothreitol (DTT), 0.5 mM EDTA, and 150 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.283
3QRF Structure of a domain-swapped FOXP3 dimer Deposited 2011-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain H 336–417（82 aa） Fragment：human FOXP3 DNA Binding Domain Chain I 336–417（82 aa） Fragment：human FOXP3 DNA Binding Domain	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.63；291 K；5 mM HEPES, pH 7.63, 2 mM dithiothreitol (DTT), 0.5 mM EDTA, and 150 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.283

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

View Construct and Data Evidence

UniProt name	FOXP3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–82； UniProt 336–417 Author chain G； PDBConstruct 1–82； UniProt 336–417

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	4wk8
Deposition date deposition_date	2014-10-01
Structure title title	FOXP3 forms a domain-swapped dimer to bridge DNA
Keywords keywords	FOXP3, regulatory T cells, DNA bridging, transcription regulation, TRANSCRIPTION-DNA complex; TRANSCRIPTION/DNA
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	23.19 Å
Radius of gyration Rg (electron density) rg_electron	21.91 Å
Forward intensity I(0) i0	27128800.00
Molecular weight molecular_weight	32416.0 kDa
Excluded volume excluded_volume	37361 Å³
Envelope volume envelope_volume	49168 Å³
Hydration-shell volume shell_volume	19939 Å³
Envelope diameter envelope_diameter	78.3 Å
Shell Rg shell_rg	27.36 Å
Envelope Rg envelope_rg	22.24 Å
Shape Rg shape_rg	21.78 Å
Total Rg total_rg	22.84 Å
Total atoms total_atoms	2243
Residues n_residues	202
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	76.8 Å
Rg (real space) rg_real	23.20 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	2.7130e+07
I(0) uncertainty (real space) i0_real_error	3.8230e+05
Rg (reciprocal space) rg_reciprocal	23.20 Å
I(0) (reciprocal space) i0_reciprocal	27130000.0000
Solution quality estimate total_estimate	0.8212
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1918000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPTPAPGPGPAPAPAPAPTPTPTPGPTPTPTPCPAPTPAP*G)-3') ;
Molecular weight formula_weight	6491.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	2243

TTAGGAAAATTTGTTTCATAG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPCPTPAPTPGPAPAPAPCPAPAPAPTPTPTPTPCPCP*T)-3') ;
Molecular weight formula_weight	6389.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

AACTATGAAACAAATTTTCCT

Entity 3 Entity 3 polymer

Description description	Forkhead box protein P3
Molecular weight formula_weight	10082.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MRPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKNAIRHNLSLHKCFVRVESEKGAVWTVDELEFRKKR

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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4wk8F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	4wk8G00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	81.431 Å
Unit-cell length b length_b	84.837 Å
Unit-cell length c length_c	68.310 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.401 Å
Low-resolution limit resolution_low	44.541 Å
R factor r_factor	0.1964
R_work r_work	0.1903
R_free r_free	0.2525

fit	/app/data/saxs_computation/wk/4wk8/4wk8.fit
pddf	/app/data/pr_computation/wk/4wk8/4wk8.pr.out
profile	/app/data/saxs_computation/wk/4wk8/4wk8.dat

FOXP3 forms a domain-swapped dimer to bridge DNA

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

Forkhead box protein P3

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)