SAXSdb — 1yo5

▼

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

SAM pointed domain containing ets transcription factor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	Enhancer site of Prostate Specific Antigen Promoter Region × 1 Enhancer site of Prostate Specific Antigen Promoter Region × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O95238_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 9–97； UniProt 247–335

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	1yo5
Deposition date deposition_date	2005-01-26
Structure title title	Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site
Keywords keywords	ETS; PROTEIN-DNA Complex; DOUBLE HELIX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1yo5__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yo5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yo5__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.39 Å
Rg (electron density)	15.26 Å
Total Rg	16.31 Å
Atom count	1286
Residues	114
Excluded volume	21440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yo5__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Enhancer site of Prostate Specific Antigen Promoter Region
Molecular weight formula_weight	4046.6 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	1442

TAGCAGGATGTGT

Entity 2 Entity 2 polymer

Description description	Enhancer site of Prostate Specific Antigen Promoter Region
Molecular weight formula_weight	3895.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

ACACATCCTGCTA

Entity 3 Entity 3 polymer

Description description	SAM pointed domain containing ets transcription factor
Molecular weight formula_weight	11587.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSLDALGSQPIHLWQFLKELLLKPHSYGRFIRWLNKEKGIFKIEDSAQVARLWGIRKNRPAMNYDKLSRSIRQYYKKGIIRKPDISQRLVYQFVHPI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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	156

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1yo5c1
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	1yo5C00
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

▶

Unit-cell length a length_a	36.160 Å
Unit-cell length b length_b	71.476 Å
Unit-cell length c length_c	39.136 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.45 °
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	2.000 Å
Low-resolution limit resolution_low	35.900 Å
R factor r_factor	0.2049
R_work r_work	0.2032
R_free r_free	0.2389

Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site

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

SAM pointed domain containing ets transcription factor

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yo5__assembly_1__model_1

1yo5__assembly_1__model_1 | I(q)

1yo5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. 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

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site

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

SAM pointed domain containing ets transcription factor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yo5__assembly_1__model_1

1yo5__assembly_1__model_1 | I(q)

1yo5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. 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

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)