SAXSdb — 1dux

▼

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

ETS-DOMAIN PROTEIN ELK-1

Homo sapiens

UniProt P19419

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 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain C； UniProt 1–94 Chain F； UniProt 1–94	Fragment：RESIDUES 1-94	;DNA (5'-D(TPGPAPCPCPGPGPAPAPGPTPGPT)-3') ; × 2 ;DNA (5'-D(APCPAPCPTPTPCPCPGPGPTPCPA)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；293 K；50 mM sodium Cacodylate, 10% PEG 2000, 100 mM MgCl2, 100 mM NaCl, 3 mM ZnCl2, pH 5.6, VAPOR DIFFUSION, temperature 293K	Resolution 2.10 Å R-free 0.236

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 1DUX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9F6Y CryoEM structure of Human Mediator subunit MED23 complexed with phosphorylated Elk-1 transcription factor Deposited 2024-05-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 308–401（94 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å

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

View Construct and Data Evidence

UniProt name	ELK1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–94； UniProt 1–94 Author chain F； PDBConstruct 1–94； UniProt 1–94

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dux
Deposition date deposition_date	2000-01-19
Structure title title	ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA-BINDING SURFACE AFFECT DNA-RECOGNITION
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

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.66 Å
Radius of gyration Rg (electron density) rg_electron	22.85 Å
Forward intensity I(0) i0	35172700.00
Molecular weight molecular_weight	36423.0 kDa
Excluded volume excluded_volume	41489 Å³
Envelope volume envelope_volume	53103 Å³
Hydration-shell volume shell_volume	20689 Å³
Envelope diameter envelope_diameter	82.0 Å
Shell Rg shell_rg	28.40 Å
Envelope Rg envelope_rg	22.71 Å
Shape Rg shape_rg	22.72 Å
Total Rg total_rg	23.70 Å
Total atoms total_atoms	2512
Residues n_residues	224
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	80.7 Å
Rg (real space) rg_real	24.82 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	3.5170e+07
I(0) uncertainty (real space) i0_real_error	5.7160e+05
Rg (reciprocal space) rg_reciprocal	24.79 Å
I(0) (reciprocal space) i0_reciprocal	35170000.0000
Solution quality estimate total_estimate	0.8785
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.437
Kurtosis Kurtosis kurtosis	-0.432
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2914000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.909

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPGPAPCPCPGPGPAPAPGPTPGP*T)-3') ;
Molecular weight formula_weight	4031.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,D
Atom count atom_count	2775

TGACCGGAAGTGT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APCPAPCPTPTPCPCPGPGPTPCP*A)-3') ;
Molecular weight formula_weight	3911.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,E

ACACTTCCGGTCA

Entity 3 Entity 3 polymer

Description description	ETS-DOMAIN PROTEIN ELK-1
Molecular weight formula_weight	11067.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDPSVTLWQFLLQLLREQGNGHIISWTSRDGGEFKLVDAEEVARLWGLRKNKTNMNYDKLSRALRYYYDKNIIRKVSGQKFVYKFVSYPEVAGC

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1duxc_
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

Domain ID domain_id	d1duxf_
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 (2 domains)

Domain ID domain_id	1duxC00
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	1duxF00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	33.245 Å
Unit-cell length b length_b	140.523 Å
Unit-cell length c length_c	38.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.52 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2020
R_free r_free	0.2360

fit	/app/data/saxs_computation/du/1dux/1dux.fit
pddf	/app/data/pr_computation/du/1dux/1dux.pr.out
profile	/app/data/saxs_computation/du/1dux/1dux.dat

ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA-BINDING SURFACE AFFECT DNA-RECOGNITION

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

ETS-DOMAIN PROTEIN ELK-1

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

6. Entities and Polymers Entities & Polymers (4)

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 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)