SAXSdb — 6od3

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

Transcription factor 4

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 405–464 Chain B； UniProt 405–464	Fragment：C-terminal bHLH domain (UNP residues 405-464)	;DNA (5'-D(CPAPTPAPCPAPCPGPTPGPTPAPT)-3') ; × 2 EDO* 1,2-ETHANEDIOL × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；25% PEG3350, 0.1 M Tris, pH 8.5, 0.2 M sodium chloride	Resolution 1.49 Å R-free 0.237
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain E； UniProt 405–464 Chain F； UniProt 405–464	Fragment：C-terminal bHLH domain (UNP residues 405-464)	;DNA (5'-D(CPAPTPAPCPAPCPGPTPGPTPAPT)-3') ; × 2 EDO* 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；25% PEG3350, 0.1 M Tris, pH 8.5, 0.2 M sodium chloride	Resolution 1.49 Å R-free 0.237
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 405–464 Chain H； UniProt 405–464	Fragment：C-terminal bHLH domain (UNP residues 405-464)	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；25% PEG3350, 0.1 M Tris, pH 8.5, 0.2 M sodium chloride	Resolution 1.49 Å R-free 0.237
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 405–464 Chain J； UniProt 405–464	Fragment：C-terminal bHLH domain (UNP residues 405-464)	EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；25% PEG3350, 0.1 M Tris, pH 8.5, 0.2 M sodium chloride	Resolution 1.49 Å R-free 0.237

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 6OD3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KWF The structure of E-protein activation domain 1 bound to the KIX domain of CBP/p300 elucidates leukemia induction by E2A-PBX1 Deposited 2010-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–27（17 aa） Fragment：UNP residues 11-27	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1 mM DSS-1, 20 mM MES-2, 1 mM beta-mercaptoethanol-3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6OD4 Human TCF4 C-terminal bHLH domain in Complex with 11-bp Oligonucleotide Containing E-box Sequence Deposited 2019-03-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 405–464（60 aa） Fragment：C-terminal bHLH domain (UNP residues 405-464) Chain B 405–464（60 aa） Fragment：C-terminal bHLH domain (UNP residues 405-464)	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；20% PEG4000, 10% 2-propanol, 0.1 M sodium citrate tribasic dihydrate, pH 5.6	Resolution 1.70 Å R-free 0.267
6OD4 Human TCF4 C-terminal bHLH domain in Complex with 11-bp Oligonucleotide Containing E-box Sequence Deposited 2019-03-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 405–464（60 aa） Fragment：C-terminal bHLH domain (UNP residues 405-464) Chain H 405–464（60 aa） Fragment：C-terminal bHLH domain (UNP residues 405-464)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；20% PEG4000, 10% 2-propanol, 0.1 M sodium citrate tribasic dihydrate, pH 5.6	Resolution 1.70 Å R-free 0.267
6OD5 Human TCF4 C-terminal bHLH domain in Complex with 12-bp Oligonucleotide Containing E-box Sequence with 5-carboxylcytosines Deposited 2019-03-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 405–464（60 aa） Fragment：C-terminal bHLH domain (UNP residues 405-464) Chain B 405–464（60 aa） Fragment：C-terminal bHLH domain (UNP residues 405-464)	Not recorded	EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；30% PEG4000, 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate monohydrate or 0.2 M sodium acetate trihydrate	Resolution 2.05 Å R-free 0.280
6OD5 Human TCF4 C-terminal bHLH domain in Complex with 12-bp Oligonucleotide Containing E-box Sequence with 5-carboxylcytosines Deposited 2019-03-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 405–464（60 aa） Fragment：C-terminal bHLH domain (UNP residues 405-464) Chain D 405–464（60 aa） Fragment：C-terminal bHLH domain (UNP residues 405-464)	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；30% PEG4000, 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate monohydrate or 0.2 M sodium acetate trihydrate	Resolution 2.05 Å R-free 0.280
8OSB TWIST1-TCF4-ALX4 complex on specific DNA Deposited 2023-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 565–624（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Sodium Cacodylate buffer (pH 7.5), 100 mM magnesium acetate, 18 % Glycerol, 20 % 2-Methyl-2,4-pentanediol, 6-7% PEG (Mw 8000)	Resolution 2.90 Å R-free 0.270

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

View Construct and Data Evidence

UniProt name	ITF2_HUMAN
Isoform	P15884-8
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–62； UniProt 405–464 Author chain B； PDBConstruct 3–62； UniProt 405–464 Author chain E； PDBConstruct 3–62； UniProt 405–464 Author chain F； PDBConstruct 3–62； UniProt 405–464 Author chain G； PDBConstruct 3–62； UniProt 405–464 Author chain H； PDBConstruct 3–62； UniProt 405–464 Author chain I； PDBConstruct 3–62； UniProt 405–464 Author chain J； PDBConstruct 3–62； UniProt 405–464

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	6od3
Deposition date deposition_date	2019-03-25
Structure title title	Human TCF4 C-terminal bHLH domain in Complex with 13-bp Oligonucleotide Containing E-box Sequence
Keywords keywords	protein-DNA complex, transcription factor, bHTH, E-Box, 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	31.34 Å
Radius of gyration Rg (electron density) rg_electron	32.48 Å
Forward intensity I(0) i0	100912000.00
Molecular weight molecular_weight	69169.0 kDa
Excluded volume excluded_volume	82540 Å³
Envelope volume envelope_volume	116560 Å³
Hydration-shell volume shell_volume	32692 Å³
Envelope diameter envelope_diameter	137.0 Å
Shell Rg shell_rg	35.60 Å
Envelope Rg envelope_rg	32.88 Å
Shape Rg shape_rg	32.53 Å
Total Rg total_rg	32.59 Å
Total atoms total_atoms	4788
Residues n_residues	523
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	129.5 Å
Rg (real space) rg_real	31.79 Å
Rg uncertainty (real space) rg_real_error	1.74 Å
I(0) (real space) i0_real	1.0090e+08
I(0) uncertainty (real space) i0_real_error	1.7100e+06
Rg (reciprocal space) rg_reciprocal	31.59 Å
I(0) (reciprocal space) i0_reciprocal	100900000.0000
Solution quality estimate total_estimate	0.7179
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.0 Å
Skewness Skewness skewness	0.767
Kurtosis Kurtosis kurtosis	0.551
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11490000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.356; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.300; Smooth: 0.960

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Transcription factor 4
Molecular weight formula_weight	7401.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F,G,H,I,J
Atom count atom_count	5160

HMRRMANNARERLRVRDINEAFKELGRMVQLHLKSDKPQTKLLILHQAVAVILSLEQQVRER

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(CPAPTPAPCPAPCPGPTPGPTPAP*T)-3') ;
Molecular weight formula_weight	3950.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X,W,Y,Z

CATACACGTGTAT

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	351

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6od3A00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	6od3B00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	6od3E00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	6od3F00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	6od3G00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	6od3H00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	6od3I00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	6od3J00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	47.180 Å
Unit-cell length b length_b	58.946 Å
Unit-cell length c length_c	62.720 Å
Unit-cell angle α angle_alpha	104.63 °
Unit-cell angle β angle_beta	90.34 °
Unit-cell angle γ angle_gamma	94.86 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.494 Å
Low-resolution limit resolution_low	37.904 Å
R factor r_factor	0.2218
R_work r_work	0.2214
R_free r_free	0.2366

fit	/app/data/saxs_computation/od/6od3/6od3.fit
pddf	/app/data/pr_computation/od/6od3/6od3.pr.out
profile	/app/data/saxs_computation/od/6od3/6od3.dat

Human TCF4 C-terminal bHLH domain in Complex with 13-bp Oligonucleotide Containing E-box Sequence

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

Transcription factor 4

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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)