SAXSdb — 6o3t

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

Forkhead box protein C2

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 A； UniProt 70–164 Chain B； UniProt 70–164	Not recorded	;DNA (5'-D(APAPAPTPTPGPTPTPTPAPTPAPAPAPCPAPGPCPCPCPG)-3') ; × 1 ;DNA (5'-D(TPTPCPGPGPGPCPTPGPTPTPTPAPTPAPAPAPCPAPAPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298.15 K；30% PEG MME 2000, 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 10 mM BME	Resolution 3.06 Å R-free 0.268

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 6O3T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5V SOLUTION STRUCTURE OF THE FORKHEAD DOMAIN OF THE ADIPOCYTE-TRANSCRIPTION FACTOR FREAC-11 (S12) Deposited 1999-10-12	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 69–162（94 aa） Fragment：DNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；300 K；Ionic strength (raw mmCIF value) 15 mM；Pressure AMBIENT NMR sample composition 1 MM S12 DBD, 10 MM NACL, 5 MM MGCL2, 0.02% NAN3, 5 MM DTT NMR sample composition 1 MM S12 DBD, 10 MM NACL, 5 MM MGCL2, 0.02% NAN3, 5 MM DTT	Resolution not provided
6AKO Crystal Structure of FOXC2 DBD Bound to DBE2 DNA Deposited 2018-09-03	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 72–172（101 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；50 mM Bis-Tris propane (pH 6.68), 14% PEG4K, 200 mM NaCl, 10 mM MgCl2, 1 mM TCEP	Resolution 2.40 Å R-free 0.250
6AKP Crystal Structural of FOXC2 DNA binding domain bound to PC promoter Deposited 2018-09-03	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 72–172（101 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；50mM NaOAc pH4.7, 14%PEG4K, 200mM NaCl, 10mM MgCl2, 0.5mM TCEP	Resolution 2.32 Å R-free 0.247
6LBM Crystal Structure of FOXC2-DBD bound to a palindromic DNA sequence Deposited 2019-11-14	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 72–172（101 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50 mM HEPES, pH 7.5, 8%-12% PEG4000 (w/v), 250 mM NaCl, 10 mM MgCl2 and 1 mM TCEP.	Resolution 2.84 Å R-free 0.263
9VRQ Crystal structure of FOXC2/NFAT1 complex bound to ARRE2 DNA Deposited 2025-07-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 72–172（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50 mM MES 5.93, 200 mM NaCl, 10 mM MgCl2, 1 mM TCEP and 12-15% PEG 4K (w/v)	Resolution 2.80 Å R-free 0.288

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

View Construct and Data Evidence

UniProt name	FOXC2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 70–164 Author chain B； PDBConstruct 1–95； UniProt 70–164

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	6o3t
Deposition date deposition_date	2019-02-27
Structure title title	Structural basis of FOXC2 and DNA interactions
Keywords keywords	Forkhead Transcription Factor DNA binding, GENE REGULATION, GENE REGULATION-DNA complex; GENE REGULATION/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	21.58 Å
Radius of gyration Rg (electron density) rg_electron	20.89 Å
Forward intensity I(0) i0	26367000.00
Molecular weight molecular_weight	31873.0 kDa
Excluded volume excluded_volume	36601 Å³
Envelope volume envelope_volume	47314 Å³
Hydration-shell volume shell_volume	19496 Å³
Envelope diameter envelope_diameter	77.6 Å
Shell Rg shell_rg	26.76 Å
Envelope Rg envelope_rg	21.25 Å
Shape Rg shape_rg	20.85 Å
Total Rg total_rg	21.67 Å
Total atoms total_atoms	2197
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	86.5 Å
Rg (real space) rg_real	21.63 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	2.6370e+07
I(0) uncertainty (real space) i0_real_error	3.7640e+05
Rg (reciprocal space) rg_reciprocal	21.62 Å
I(0) (reciprocal space) i0_reciprocal	26370000.0000
Solution quality estimate total_estimate	0.6922
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.440
Kurtosis Kurtosis kurtosis	-0.144
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3868000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.467; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.593; 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	Forkhead box protein C2
Molecular weight formula_weight	11266.9 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	2197

LVKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNECFVKVPRDDKKPGKGSYWTLDPDSYNMFENGSFLRR

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPAPTPTPGPTPTPTPAPTPAPAPAPCPAPGPCPCPCP*G)-3') ;
Molecular weight formula_weight	6430.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

AAATTGTTTATAAACAGCCCG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(TPTPCPGPGPGPCPTPGPTPTPTPAPTPAPAPAPCPAPAP*T)-3') ;
Molecular weight formula_weight	6452.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TTCGGGCTGTTTATAAACAAT

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6o3tA00
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	6o3tB00
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	128.365 Å
Unit-cell length b length_b	41.812 Å
Unit-cell length c length_c	82.654 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.060 Å
Low-resolution limit resolution_low	36.377 Å
R factor r_factor	0.2349
R_work r_work	0.2332
R_free r_free	0.2683

fit	/app/data/saxs_computation/o3/6o3t/6o3t.fit
pddf	/app/data/pr_computation/o3/6o3t/6o3t.pr.out
profile	/app/data/saxs_computation/o3/6o3t/6o3t.dat

Structural basis of FOXC2 and DNA interactions

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

Forkhead box protein C2

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)