SAXSdb — 8yth

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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	Zinc finger and BTB domain-containing protein 16 × 1 （Q05516） 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

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 8YTH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8YTF Crystal structures of human IRF2BP2 RING domain in complex with VGLL4 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；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
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

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

Zinc finger and BTB domain-containing protein 16

OrganismNot specified

UniProt Q05516

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 285–292	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；0.1 M potassium thiocyanate and 30% (w/v) PEG MME 2000	Resolution 2.40 Å R-free 0.281

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 8YTH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BUO BTB DOMAIN FROM PLZF Deposited 1998-09-04	Different construct 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 6–126（121 aa） Fragment：BTB DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.15 M CACL2, 0.1 M HEPES (PH 7.5), 4% ISOPROPANOL,	Resolution 1.90 Å R-free 0.252
1CS3 STRUCTURE OF BTB/POZ TRANSCRIPTION REPRESSION DOMAIN FROM PROMELOCYTIC LEUKEMIA ZINC FINGER ONCOPROTEIN Deposited 1999-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–122（116 aa） Fragment：BTB/POZ	Not recorded	MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；VAPOR DIFFUSION BY 8% ISOPROPANOL, 600mM MAGNESIUM CHLORIDE, 50mM HEPES 7.5 and 50mM TRIS 8.5, pH 8.00	Resolution 2.00 Å R-free 0.272
1CS3 STRUCTURE OF BTB/POZ TRANSCRIPTION REPRESSION DOMAIN FROM PROMELOCYTIC LEUKEMIA ZINC FINGER ONCOPROTEIN Deposited 1999-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 7–122（116 aa） Fragment：BTB/POZ	Not recorded	MG MAGNESIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；VAPOR DIFFUSION BY 8% ISOPROPANOL, 600mM MAGNESIUM CHLORIDE, 50mM HEPES 7.5 and 50mM TRIS 8.5, pH 8.00	Resolution 2.00 Å R-free 0.272

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

View Construct and Data Evidence

UniProt name	ZBT16_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–8； UniProt 285–292

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	8yth
Deposition date deposition_date	2024-03-25
Structure title title	Crystal structures of human IRF2BP2 RING domain in complex with ZBTB16 peptide
Keywords keywords	IRF2BP2, RING domain, ZBTB16, 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	12.41 Å
Radius of gyration Rg (electron density) rg_electron	11.16 Å
Forward intensity I(0) i0	1669610.00
Molecular weight molecular_weight	8208.0 kDa
Excluded volume excluded_volume	9993 Å³
Envelope volume envelope_volume	10734 Å³
Hydration-shell volume shell_volume	8421 Å³
Envelope diameter envelope_diameter	38.4 Å
Shell Rg shell_rg	16.48 Å
Envelope Rg envelope_rg	11.48 Å
Shape Rg shape_rg	11.17 Å
Total Rg total_rg	12.44 Å
Total atoms total_atoms	560
Residues n_residues	76
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	39.7 Å
Rg (real space) rg_real	12.33 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.6700e+06
I(0) uncertainty (real space) i0_real_error	1.7420e+04
Rg (reciprocal space) rg_reciprocal	12.33 Å
I(0) (reciprocal space) i0_reciprocal	1670000.0000
Solution quality estimate total_estimate	0.8846
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.6 Å
Skewness Skewness skewness	0.112
Kurtosis Kurtosis kurtosis	-0.340
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	190100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.952

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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	561

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	Zinc finger and BTB domain-containing protein 16
Molecular weight formula_weight	820.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

RSSVITSA

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	1

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8. Citations (1)

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Unit-cell length a length_a	47.315 Å
Unit-cell length b length_b	47.315 Å
Unit-cell length c length_c	57.489 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	33.370 Å
R factor r_factor	0.2447
R_work r_work	0.2430
R_free r_free	0.2807

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

Crystal structures of human IRF2BP2 RING domain in complex with ZBTB16 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

Zinc finger and BTB domain-containing protein 16

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)