SAXSdb — 3ixs

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

E3 ubiquitin-protein ligase RING2

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	RING1 and YY1-binding protein × 1 （Q8N488） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	RING1 and YY1-binding protein × 1 （Q8N488） 1,2-ETHANEDIOL × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	RING1 and YY1-binding protein × 1 （Q8N488） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	RING1 and YY1-binding protein × 1 （Q8N488） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	RING1 and YY1-binding protein × 1 （Q8N488） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	RING1 and YY1-binding protein × 1 （Q8N488） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RING2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–111； UniProt 223–333 Author chain C； PDBConstruct 1–111； UniProt 223–333 Author chain E； PDBConstruct 1–111； UniProt 223–333 Author chain G； PDBConstruct 1–111； UniProt 223–333 Author chain I； PDBConstruct 1–111； UniProt 223–333 Author chain K； PDBConstruct 1–111； UniProt 223–333

RING1 and YY1-binding protein

Homo sapiens

UniProt Q8N488

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RING2 × 1 （Q99496） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RING2 × 1 （Q99496） 1,2-ETHANEDIOL × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RING2 × 1 （Q99496） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RING2 × 1 （Q99496） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RING2 × 1 （Q99496） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RING2 × 1 （Q99496） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RYBP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–37； UniProt 145–179 Author chain D； PDBConstruct 3–37； UniProt 145–179 Author chain F； PDBConstruct 3–37； UniProt 145–179 Author chain H； PDBConstruct 3–37； UniProt 145–179 Author chain J； PDBConstruct 3–37； UniProt 145–179 Author chain L； PDBConstruct 3–37； UniProt 145–179

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	3ixs
Deposition date deposition_date	2009-09-04
Structure title title	Ring1B C-terminal domain/RYBP C-terminal domain Complex
Keywords keywords	;RING1B, RYBP, polycomb, e3-ligase, chromosomal protein, transcription regulation, chromatin regulator, transcription repressor, Ligase, Metal-binding, Nucleus, Phosphoprotein, Repressor, Transcription, Ubl conjugation pathway, Zinc-finger, Apoptosis, DNA-binding, PROTEIN BINDING ;; PROTEIN BINDING
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.

3ixs__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ixs__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ixs__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	15.58 Å
Rg (electron density)	14.07 Å
Total Rg	15.45 Å
Atom count	1066
Residues	133
Excluded volume	19125 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ixs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ixs__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ixs__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ixs__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3ixs__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3ixs__assembly_6__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	E3 ubiquitin-protein ligase RING2
Molecular weight formula_weight	12614.2 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	N306D
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	6935

ASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLDGSFSLELVSEKYWKVNKPMELYYAPTK

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	RING1 and YY1-binding protein
Molecular weight formula_weight	4107.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

GTRPRLKNVDRSTAQQLAVTVGNVTVIITDFKEKTRS

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 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
Molecular weight formula_weight	207.3 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	421

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3ixsA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3ixsC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3ixsE00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3ixsG00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3ixsI00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3ixsK00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	37.894 Å
Unit-cell length b length_b	56.549 Å
Unit-cell length c length_c	100.352 Å
Unit-cell angle α angle_alpha	100.88 °
Unit-cell angle β angle_beta	90.61 °
Unit-cell angle γ angle_gamma	100.49 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	40.676 Å
R factor r_factor	0.2045
R_work r_work	0.2030
R_free r_free	0.2339

Ring1B C-terminal domain/RYBP C-terminal domain Complex

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

E3 ubiquitin-protein ligase RING2

State in the Current Structure

Other States of the Same Protein in the Database

RING1 and YY1-binding protein

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

3ixs__assembly_3__model_1

3ixs__assembly_3__model_1 | I(q)

3ixs__assembly_3__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Ring1B C-terminal domain/RYBP C-terminal domain Complex

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

E3 ubiquitin-protein ligase RING2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RING1 and YY1-binding 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ixs__assembly_3__model_1

3ixs__assembly_3__model_1 | I(q)

3ixs__assembly_3__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)