4oyj

Structure of the apo HOIP PUB domain

Method: X-RAY DIFFRACTION

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

E3 ubiquitin-protein ligase RNF31

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
13	Protein monomer	Monomer	Protein 1	SULFATE ION × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 4	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 4 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SULFATE ION × 4 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	SULFATE ION × 2	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNF31_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–186； UniProt 1–184 Author chain B； PDBConstruct 3–186； UniProt 1–184 Author chain C； PDBConstruct 3–186； UniProt 1–184 Author chain D； PDBConstruct 3–186； UniProt 1–184 Author chain E； PDBConstruct 3–186； UniProt 1–184 Author chain F； PDBConstruct 3–186； UniProt 1–184 Author chain G； PDBConstruct 3–186； UniProt 1–184 Author chain H； PDBConstruct 3–186； UniProt 1–184 Author chain I； PDBConstruct 3–186； UniProt 1–184 Author chain J； PDBConstruct 3–186； UniProt 1–184 Author chain K； PDBConstruct 3–186； UniProt 1–184 Author chain L； PDBConstruct 3–186； UniProt 1–184 Author chain M； PDBConstruct 3–186； UniProt 1–184

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	4oyj
Deposition date deposition_date	2014-02-12
Structure title title	Structure of the apo HOIP PUB domain
Keywords keywords	E3 ubiquitin ligase, PUB domain, LIGASE; 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.

4oyj__assembly_8__model_1

Assembly 8 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4oyj__assembly_8__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4oyj__assembly_8__model_1 | P(r) · Pending

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

Rg（Guinier）	17.69 Å
Rg (electron density)	16.25 Å
Total Rg	17.29 Å
Atom count	1367
Residues	178
Excluded volume	24133 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4oyj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4oyj__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4oyj__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4oyj__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4oyj__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4oyj__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4oyj__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`4oyj__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`4oyj__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`4oyj__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`4oyj__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`4oyj__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`4oyj__assembly_13__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase RNF31
Molecular weight formula_weight	21101.7 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M
Atom count atom_count	18399

GPMPGEEEERAFLVAREELASALRRDSGQAFSLEQLRPLLASSLPLAARYLQLDAARLVRCNAHGEPRNYLNTLSTALNILEKYGRNLLSPQRPRYWRGVKFNNPVFRSTVDAVQGGRDVLRLYGYTEEQPDGLSFPEGQEEPDEHQVATVTLEVLLLRTELSLLLQNTHPRQQALEQLLEDKVED

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	30

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id	4oyjA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjM00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

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Unit-cell length a length_a	155.190 Å
Unit-cell length b length_b	99.540 Å
Unit-cell length c length_c	173.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	52

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	62.605 Å
R factor r_factor	0.2094
R_work r_work	0.2070
R_free r_free	0.2545

Structure of the apo HOIP PUB domain

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

E3 ubiquitin-protein ligase RNF31

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

4oyj__assembly_8__model_1

4oyj__assembly_8__model_1 | I(q)

4oyj__assembly_8__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. Citations (1)

Structure of the apo HOIP PUB domain

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

E3 ubiquitin-protein ligase RNF31

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

4oyj__assembly_8__model_1

4oyj__assembly_8__model_1 | I(q)

4oyj__assembly_8__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. Citations (1)