SAXSdb — 4pw7

▼

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

E3 ubiquitin-protein ligase UHRF2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	5mC-containing DNA1 × 1 5mC-containing DNA2 × 1 water × 4	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	5mC-containing DNA1 × 1 5mC-containing DNA2 × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UHRF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–230； UniProt 419–648 Author chain B； PDBConstruct 1–230； UniProt 419–648 Author chain E； PDBConstruct 1–230； UniProt 419–648 Author chain F； PDBConstruct 1–230； UniProt 419–648

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4pw7
Deposition date deposition_date	2014-03-19
Structure title title	structure of UHRF2-SRA in complex with a 5mC-containing DNA
Keywords keywords	SRA, 5hmC binding, 5hmC-containing DNA, methylation, nuclear, LIGASE-DNA complex; LIGASE/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4pw7__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4pw7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pw7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.88 Å
Rg (electron density)	26.99 Å
Total Rg	27.58 Å
Atom count	3549
Residues	412
Excluded volume	60825 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pw7__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4pw7__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase UHRF2
Molecular weight formula_weight	25579.7 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F
Atom count atom_count	8173

STESRRDWGRGMACVGRTRECTIVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGGKNLAGNKRIGAPSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGYPSDKEGK

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	5mC-containing DNA1
Molecular weight formula_weight	3708.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,G

CTGGTCCGGATG

Entity 3 Entity 3 polymer

Description description	5mC-containing DNA2
Molecular weight formula_weight	3592.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H

CCATCCGGACCA

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	932

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4pw7a_
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.12 — SRA domain-like

Domain ID domain_id	d4pw7b_
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.12 — SRA domain-like

Domain ID domain_id	d4pw7e_
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.12 — SRA domain-like

Domain ID domain_id	d4pw7f_
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.12 — SRA domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	4pw7A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	280 — PUA domain-like
Homologous superfamily homologous superfamily	10 — SRA-YDG

Domain ID domain_id	4pw7B01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	280 — PUA domain-like
Homologous superfamily homologous superfamily	10 — SRA-YDG

Domain ID domain_id	4pw7E01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	280 — PUA domain-like
Homologous superfamily homologous superfamily	10 — SRA-YDG

Domain ID domain_id	4pw7F01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	280 — PUA domain-like
Homologous superfamily homologous superfamily	10 — SRA-YDG

▶

Unit-cell length a length_a	42.331 Å
Unit-cell length b length_b	83.694 Å
Unit-cell length c length_c	83.686 Å
Unit-cell angle α angle_alpha	89.97 °
Unit-cell angle β angle_beta	89.94 °
Unit-cell angle γ angle_gamma	90.02 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.001 Å
Low-resolution limit resolution_low	28.050 Å
R factor r_factor	0.1657
R_work r_work	0.1634
R_free r_free	0.2108

structure of UHRF2-SRA in complex with a 5mC-containing DNA

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

E3 ubiquitin-protein ligase UHRF2

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

4pw7__assembly_2__model_1

4pw7__assembly_2__model_1 | I(q)

4pw7__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

structure of UHRF2-SRA in complex with a 5mC-containing DNA

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

E3 ubiquitin-protein ligase UHRF2

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

4pw7__assembly_2__model_1

4pw7__assembly_2__model_1 | I(q)

4pw7__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)