SAXSdb — 5ybd

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

Transcriptional regulator ERG

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 A； UniProt 317–406	Fragment：ETS domain, UNP residues 317-406	;DNA (5'-D(PAPCPCPGPGPAPAPGPT)-3') ; × 1 ;DNA (5'-D(PCPAPCPTPTPCPCPGPGP*T)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20%(w/v) PEG4000, 200mM MgCl2 as precipitant solution	Resolution 2.77 Å R-free 0.282
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain X； UniProt 317–406	Fragment：ETS domain, UNP residues 317-406	;DNA (5'-D(PAPCPCPGPGPAPAPGPT)-3') ; × 1 ;DNA (5'-D(PCPAPCPTPTPCPCPGPGP*T)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20%(w/v) PEG4000, 200mM MgCl2 as precipitant solution	Resolution 2.77 Å R-free 0.282

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 5YBD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SXE The solution structure of the Pointed (PNT) domain from the transcrition factor Erg Deposited 2004-03-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–208（94 aa） Fragment：PNT domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR sample composition 1mM Erg U-15N,13C, 20mM phosphate buffer pH 7.0, 50mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM Erg 100%15N,10%13C, 20mM phosphate buffer pH 7.0, 50mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2mM Erg 100%15N, 20mM phosphate buffer pH 7.0, 50mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2mM Erg 100%15N, 20mM phosphate buffer pH 7.0, 50mM NaCl, 2mM DTT, 1% H2O, 99% D2O \| 1% H2O, 99% D2O	Resolution not provided
4IRG Uninhibited DNA-binding domain of the Ets transcription factor ERG Deposited 2013-01-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 313–412（100 aa） Fragment：Ets Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；290 K；1.4M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 1.70 Å R-free 0.228
4IRH Auto-inhibited ERG Ets domain Deposited 2013-01-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 287–412（126 aa） Fragment：Ets Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；290 K；1.4M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.10 Å R-free 0.215
4IRI Auto-inhibited ERG Ets Domain-DNA Complex Deposited 2013-01-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 287–412（126 aa） Fragment：Ets Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.2M ammonium chloride, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.77 Å R-free 0.210
5YBC X-ray structure of native ETS-domain domain of Ergp55 Deposited 2017-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 317–408（92 aa） Fragment：ETS domain, UNP residues 317-408 Chain C 317–408（92 aa） Fragment：ETS domain, UNP residues 317-408	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；20%(w/v) PEG400, 130mM NaCl, 60mM MgCl2, 100mM sodium citrate pH 5.6	Resolution 2.50 Å R-free 0.257
6VGE Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 313–426（114 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.25 Å R-free 0.317
6VGG Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-08	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 313–426（114 aa） Fragment：DNA binding domain	Not recorded	QWP mithramycin × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.3 M K/Na Tartrate, 50 mM Hepes, pH 7.0, soaked in 1 mM mithramycin-Mg	Resolution 4.31 Å R-free 0.285

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ERG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–90； UniProt 317–406 Author chain X； PDBConstruct 1–90； UniProt 317–406

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	5ybd
Deposition date deposition_date	2017-09-04
Structure title title	X-ray structure of ETS domain of Ergp55 in complex with E74DNA
Keywords keywords	ETS transcription factor, human Ergp55, ETS-E74DNA complex, DNA BINDING PROTEIN-DNA complex, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	22.68 Å
Radius of gyration Rg (electron density) rg_electron	22.19 Å
Forward intensity I(0) i0	30583300.00
Molecular weight molecular_weight	34431.0 kDa
Excluded volume excluded_volume	39502 Å³
Envelope volume envelope_volume	51084 Å³
Hydration-shell volume shell_volume	19758 Å³
Envelope diameter envelope_diameter	79.6 Å
Shell Rg shell_rg	28.09 Å
Envelope Rg envelope_rg	22.58 Å
Shape Rg shape_rg	22.18 Å
Total Rg total_rg	22.82 Å
Total atoms total_atoms	2379
Residues n_residues	228
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	77.4 Å
Rg (real space) rg_real	22.71 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	3.0580e+07
I(0) uncertainty (real space) i0_real_error	4.0640e+05
Rg (reciprocal space) rg_reciprocal	22.71 Å
I(0) (reciprocal space) i0_reciprocal	30580000.0000
Solution quality estimate total_estimate	0.7047
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.379
Kurtosis Kurtosis kurtosis	-0.362
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3708000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.950; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Transcriptional regulator ERG
Molecular weight formula_weight	11651.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,X
Atom count atom_count	2379

QIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALLEHHHHH

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	Enterobacteria phage L1

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PAPCPCPGPGPAPAPGP*T)-3') ;
Molecular weight formula_weight	2764.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,Y

ACCGGAAGT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PCPAPCPTPTPCPCPGPGPT)-3') ;
Molecular weight formula_weight	2996.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,Z

CACTTCCGGT

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ybdA00
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	5ybdX00
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	39.279 Å
Unit-cell length b length_b	233.871 Å
Unit-cell length c length_c	80.524 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.769 Å
Low-resolution limit resolution_low	38.978 Å
R factor r_factor	0.2081
R_work r_work	0.2044
R_free r_free	0.2816

fit	/app/data/saxs_computation/yb/5ybd/5ybd.fit
pddf	/app/data/pr_computation/yb/5ybd/5ybd.pr.out
profile	/app/data/saxs_computation/yb/5ybd/5ybd.dat

X-ray structure of ETS domain of Ergp55 in complex with E74DNA

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

Transcriptional regulator ERG

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)