SAXSdb — 3ivb

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

Speckle-type POZ protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Core histone macro-H2A.1 × 1 （O75367） ZINC ION × 5 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPOP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–145； UniProt 28–166

Core histone macro-H2A.1

OrganismNot specified

UniProt O75367

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Speckle-type POZ protein × 1 （O43791） ZINC ION × 5 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2AY_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–15； UniProt 167–181

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	3ivb
Deposition date deposition_date	2009-08-31
Structure title title	Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1
Keywords keywords	;Protein Binding/Hydrolase, Nucleus, Ubl conjugation pathway, Alternative splicing, Chromatin regulator, Chromosomal protein, DNA-binding, Isopeptide bond, Methylation, Nucleosome core, Phosphoprotein, Ubl conjugation, protein binding, ligase ;; protein binding, ligase
Experimental Method method	X-RAY DIFFRACTION

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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.

3ivb__assembly_1__model_1

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

Download this curve (.dat)

3ivb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ivb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.71 Å
Rg (electron density)	15.12 Å
Total Rg	16.51 Å
Atom count	1180
Residues	148
Excluded volume	21181 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ivb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Speckle-type POZ protein
Molecular weight formula_weight	16544.0 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	1307

GSGGSGKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQD

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 2 Entity 2 polymer

Description description	Core histone macro-H2A.1
Molecular weight formula_weight	1422.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

KAASADSTTEGTPAD

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	5

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ivba_
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

CATH v4.4 (1 domains)

Domain ID domain_id	3ivbA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

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Unit-cell length a length_a	44.021 Å
Unit-cell length b length_b	44.021 Å
Unit-cell length c length_c	266.840 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	37.740 Å
R factor r_factor	0.2196
R_work r_work	0.2183
R_free r_free	0.2473

Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1

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

Speckle-type POZ protein

State in the Current Structure

Other States of the Same Protein in the Database

Core histone macro-H2A.1

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

3ivb__assembly_1__model_1

3ivb__assembly_1__model_1 | I(q)

3ivb__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1

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

Speckle-type POZ protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Core histone macro-H2A.1

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

3ivb__assembly_1__model_1

3ivb__assembly_1__model_1 | I(q)

3ivb__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)