SAXSdb — 1bc8

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

PROTEIN (SAP-1 ETS DOMAIN)

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 1–93	Fragment：ETS DOMAIN, RESIDUES 1-93	;DNA (5'-D(TPAPCPCPGPGPAPAPGPT)-3') ; × 1 ;DNA (5'-D(APAPCPTPTPCPCPGPGPT)-3') ; × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；50 MM NA CACODYLATE (PH 6.0), 5.0% PEG8000, 20 MM ZINC ACETATE	Resolution 1.93 Å R-free 0.277

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 1BC8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BC7 SERUM RESPONSE FACTOR ACCESSORY PROTEIN 1A (SAP-1)/DNA COMPLEX Deposited 1998-05-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–93（93 aa） Fragment：ETS DOMAIN, RESIDUES 1-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；pH 5.8	Resolution 2.01 Å R-free 0.286
1HBX Ternary Complex of SAP-1 and SRF with specific SRE DNA Deposited 2001-04-20	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 G 2–156（155 aa） Fragment：RESIDUES 2-156	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50	Resolution 3.15 Å R-free 0.285
1HBX Ternary Complex of SAP-1 and SRF with specific SRE DNA Deposited 2001-04-20	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 2–156（155 aa） Fragment：RESIDUES 2-156	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50	Resolution 3.15 Å R-free 0.285
1K6O Crystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex Deposited 2001-10-16	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 A 1–93（93 aa） Fragment：1-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP	Resolution 3.19 Å R-free 0.276

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

View Construct and Data Evidence

UniProt name	ELK4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–93； UniProt 1–93

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	1bc8
Deposition date deposition_date	1998-05-05
Structure title title	STRUCTURES OF SAP-1 BOUND TO DNA SEQUENCES FROM THE E74 AND C-FOS PROMOTERS PROVIDE INSIGHTS INTO HOW ETS PROTEINS DISCRIMINATE BETWEEN RELATED DNA TARGETS
Keywords keywords	ETS DOMAIN, DNA-BINDING DOMAIN, WINGED HELIX-TURN-HELIX, DNA-BINDING SPECIFICITY, 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	16.18 Å
Radius of gyration Rg (electron density) rg_electron	14.82 Å
Forward intensity I(0) i0	8046570.00
Molecular weight molecular_weight	17414.0 kDa
Excluded volume excluded_volume	20321 Å³
Envelope volume envelope_volume	23467 Å³
Hydration-shell volume shell_volume	13461 Å³
Envelope diameter envelope_diameter	49.4 Å
Shell Rg shell_rg	20.67 Å
Envelope Rg envelope_rg	15.10 Å
Shape Rg shape_rg	14.69 Å
Total Rg total_rg	16.07 Å
Total atoms total_atoms	1196
Residues n_residues	113
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	50.6 Å
Rg (real space) rg_real	16.09 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	8.0470e+06
I(0) uncertainty (real space) i0_real_error	9.1140e+04
Rg (reciprocal space) rg_reciprocal	16.10 Å
I(0) (reciprocal space) i0_reciprocal	8047000.0000
Solution quality estimate total_estimate	0.9042
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.165
Kurtosis Kurtosis kurtosis	-0.421
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	849100.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.998

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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(TPAPCPCPGPGPAPAPGPT)-3') ;
Molecular weight formula_weight	3069.0 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	1356

TACCGGAAGT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPCPTPTPCPCPGPGPT)-3') ;
Molecular weight formula_weight	3020.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

AACTTCCGGT

Entity 3 Entity 3 polymer

Description description	PROTEIN (SAP-1 ETS DOMAIN)
Molecular weight formula_weight	11219.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MDSAITLWQFLLQLLQKPQNKHMICWTSNDGQFKLLQAEEVARLWGIRKNKPNMNYDKLSRALRYYYVKNIIKKVNGQKFVYKFVSYPEILNM

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	160

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bc8c_
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.4.5.21 — ets domain

CATH v4.4 (1 domains)

Domain ID domain_id	1bc8C00
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	31.590 Å
Unit-cell length b length_b	55.670 Å
Unit-cell length c length_c	44.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	28.900 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2770

fit	/app/data/saxs_computation/bc/1bc8/1bc8.fit
pddf	/app/data/pr_computation/bc/1bc8/1bc8.pr.out
profile	/app/data/saxs_computation/bc/1bc8/1bc8.dat

STRUCTURES OF SAP-1 BOUND TO DNA SEQUENCES FROM THE E74 AND C-FOS PROMOTERS PROVIDE INSIGHTS INTO HOW ETS PROTEINS DISCRIMINATE BETWEEN RELATED DNA TARGETS

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

PROTEIN (SAP-1 ETS DOMAIN)

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 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)