SAXSdb — 8ytf

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

Interferon regulatory factor 2-binding protein 2

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 497–578	Fragment：RING domain	Transcription cofactor vestigial-like protein 4 × 1 （Q14135） ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；20% 2-proponal, 0.1 M MES (pH 6.0) and 20% (w/v) PEG MME 2000	Resolution 1.59 Å R-free 0.173

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 8YTF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8YTG Crystal structures of human IRF2BP2 RING domain in complex with IRF2 peptide Deposited 2024-03-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 497–578（82 aa） Fragment：RING domain	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.5 M ammonium sulfate and 0.1 M sodium acetate (pH 4.6)	Resolution 1.45 Å R-free 0.189
8YTH Crystal structures of human IRF2BP2 RING domain in complex with ZBTB16 peptide Deposited 2024-03-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 497–578（82 aa） Fragment：RING domain	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M potassium thiocyanate and 30% (w/v) PEG MME 2000	Resolution 2.40 Å R-free 0.281

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

View Construct and Data Evidence

UniProt name	I2BP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–83； UniProt 497–578

Transcription cofactor vestigial-like protein 4

OrganismNot specified

UniProt Q14135

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 161–168	Not recorded	Interferon regulatory factor 2-binding protein 2 × 1 （Q7Z5L9） ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；20% 2-proponal, 0.1 M MES (pH 6.0) and 20% (w/v) PEG MME 2000	Resolution 1.59 Å R-free 0.173

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	VGLL4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–8； UniProt 161–168

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	8ytf
Deposition date deposition_date	2024-03-25
Structure title title	Crystal structures of human IRF2BP2 RING domain in complex with VGLL4 peptide
Keywords keywords	IRF2BP2, RING domain, VGLL4, TRANSCRIPTION; TRANSCRIPTION
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	13.98 Å
Radius of gyration Rg (electron density) rg_electron	12.76 Å
Forward intensity I(0) i0	2117600.00
Molecular weight molecular_weight	9464.0 kDa
Excluded volume excluded_volume	11586 Å³
Envelope volume envelope_volume	12989 Å³
Hydration-shell volume shell_volume	9185 Å³
Envelope diameter envelope_diameter	49.4 Å
Shell Rg shell_rg	17.80 Å
Envelope Rg envelope_rg	13.33 Å
Shape Rg shape_rg	12.66 Å
Total Rg total_rg	14.14 Å
Total atoms total_atoms	648
Residues n_residues	86
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	51.4 Å
Rg (real space) rg_real	14.00 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	2.1180e+06
I(0) uncertainty (real space) i0_real_error	2.4820e+04
Rg (reciprocal space) rg_reciprocal	14.00 Å
I(0) (reciprocal space) i0_reciprocal	2118000.0000
Solution quality estimate total_estimate	0.8134
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.3 Å
Skewness Skewness skewness	0.458
Kurtosis Kurtosis kurtosis	0.190
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	261900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.562; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Interferon regulatory factor 2-binding protein 2
Molecular weight formula_weight	8867.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	776

GSLATSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRQSIKQQGASGEVYCPSGEKCPLVGSNVPWAFMQGEIATILAGD

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 2 Entity 2 polymer

Description description	Transcription cofactor vestigial-like protein 4
Molecular weight formula_weight	847.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

RPSVITCA

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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8. Citations (1)

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Unit-cell length a length_a	33.372 Å
Unit-cell length b length_b	43.209 Å
Unit-cell length c length_c	55.761 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.590 Å
Low-resolution limit resolution_low	23.430 Å
R factor r_factor	0.1536
R_work r_work	0.1527
R_free r_free	0.1727

fit	/app/data/saxs_computation/yt/8ytf/8ytf.fit
pddf	/app/data/pr_computation/yt/8ytf/8ytf.pr.out
profile	/app/data/saxs_computation/yt/8ytf/8ytf.dat

Crystal structures of human IRF2BP2 RING domain in complex with VGLL4 peptide

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

Interferon regulatory factor 2-binding protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Transcription cofactor vestigial-like protein 4

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)