SAXSdb — 1cf7

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

PROTEIN (TRANSCRIPTION FACTOR E2F-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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 11–86	Fragment：DNA-BINDING DOMAIN	;DNA (5'-D(APTPTPTPTPCPGPCPGPCPGPGPTPTPTPT)-3') ; × 1 ;DNA (5'-D(TPAPAPAPAPCPCPGPCPGPCPGPAPAPAPA)-3') ; × 1 PROTEIN (TRANSCRIPTION FACTOR DP-2) × 1 （Q14188）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；277 K；14-16% PEG 400, 25MM NACL, 50MM MES, 10MM DTT, PH=6.0, 4 DEGREES C, temperature 277K	Resolution 2.60 Å

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 1CF7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5TUU Crystal structure of the E2F4-DP1 coiled coil and marked-box domains Deposited 2016-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 91–198（108 aa） Fragment：UNP residues 91-198	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES pH 6.5, 15% PEG 6000	Resolution 2.25 Å R-free 0.239
5TUU Crystal structure of the E2F4-DP1 coiled coil and marked-box domains Deposited 2016-11-07	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 B 91–198（108 aa） Fragment：UNP residues 91-198	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES pH 6.5, 15% PEG 6000	Resolution 2.25 Å R-free 0.239

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

View Construct and Data Evidence

UniProt name	E2F4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 11–86

PROTEIN (TRANSCRIPTION FACTOR DP-2)

Homo sapiens

UniProt Q14188

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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 60–154	Fragment：DNA-BINDING DOMAIN	;DNA (5'-D(APTPTPTPTPCPGPCPGPCPGPGPTPTPTPT)-3') ; × 1 ;DNA (5'-D(TPAPAPAPAPCPCPGPCPGPCPGPAPAPAPA)-3') ; × 1 PROTEIN (TRANSCRIPTION FACTOR E2F-4) × 1 （Q16254）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；277 K；14-16% PEG 400, 25MM NACL, 50MM MES, 10MM DTT, PH=6.0, 4 DEGREES C, temperature 277K	Resolution 2.60 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	TDP2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–95； UniProt 60–154

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	1cf7
Deposition date deposition_date	1999-03-24
Structure title title	STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP
Keywords keywords	E2F, DP, WINGED-HELIX, DNA-BINDING DOMAIN, TRANSCRIPTION FACTOR, CELL CYCLE, 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	18.62 Å
Radius of gyration Rg (electron density) rg_electron	17.61 Å
Forward intensity I(0) i0	17955200.00
Molecular weight molecular_weight	26136.0 kDa
Excluded volume excluded_volume	30197 Å³
Envelope volume envelope_volume	37464 Å³
Hydration-shell volume shell_volume	17855 Å³
Envelope diameter envelope_diameter	59.1 Å
Shell Rg shell_rg	23.60 Å
Envelope Rg envelope_rg	17.79 Å
Shape Rg shape_rg	17.56 Å
Total Rg total_rg	18.50 Å
Total atoms total_atoms	1798
Residues n_residues	179
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	58.6 Å
Rg (real space) rg_real	18.52 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	1.7960e+07
I(0) uncertainty (real space) i0_real_error	2.2580e+05
Rg (reciprocal space) rg_reciprocal	18.54 Å
I(0) (reciprocal space) i0_reciprocal	17960000.0000
Solution quality estimate total_estimate	0.9000
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.149
Kurtosis Kurtosis kurtosis	-0.433
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2279000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APTPTPTPTPCPGPCPGPCPGPGPTPTPTPT)-3') ;
Molecular weight formula_weight	4886.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	1873

ATTTTCGCGCGGTTTT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPAPAPAPAPCPCPGPCPGPCPGPAPAPAPA)-3') ;
Molecular weight formula_weight	4909.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TAAAACCGCGCGAAAA

Entity 3 Entity 3 polymer

Description description	PROTEIN (TRANSCRIPTION FACTOR E2F-4)
Molecular weight formula_weight	8352.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

PPGTPSRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKSKNSIQWKGVGP

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

Entity 4 Entity 4 polymer

Description description	PROTEIN (TRANSCRIPTION FACTOR DP-2)
Molecular weight formula_weight	10836.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

RSKKGDKNGKGLRHFSMKVCEKVQRKGTTSYNEVADELVSEFTNSNNHLAADSAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQ

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	75

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cf7a_
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.4.5.17 — Cell cycle transcription factor e2f-dp

Domain ID domain_id	d1cf7b_
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.4.5.17 — Cell cycle transcription factor e2f-dp

CATH v4.4 (2 domains)

Domain ID domain_id	1cf7A00
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	1cf7B00
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	101.300 Å
Unit-cell length b length_b	101.300 Å
Unit-cell length c length_c	73.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2230
R_free r_free	—

fit	/app/data/saxs_computation/cf/1cf7/1cf7.fit
pddf	/app/data/pr_computation/cf/1cf7/1cf7.pr.out
profile	/app/data/saxs_computation/cf/1cf7/1cf7.dat

STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP

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

PROTEIN (TRANSCRIPTION FACTOR E2F-4)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (TRANSCRIPTION FACTOR DP-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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)