SAXSdb — 3db3

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

E3 ubiquitin-protein ligase UHRF1

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	Trimethylated histone H3-K9 peptide × 1 （Q71DI3） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UHRF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–161； UniProt 126–285

Trimethylated histone H3-K9 peptide

OrganismNot specified

UniProt Q71DI3

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 UHRF1 × 1 （Q96T88） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–6； UniProt 7–12

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	3db3
Deposition date deposition_date	2008-05-30
Structure title title	Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide
Keywords keywords	;CELL CYCLE, DNA DAMAGE, DNA REPAIR, TANDEM TUDOR DOMAINS, LIGASE, METAL BINDING, DNA REPLICATION, TRANSCRIPTIONAL SILENCING, CHROMATIN, PHOSPHORYLATION, TRANSCRIPTION, TRANSCRIPTION REGULATION, UBL CONJUGATION PATHWAY, ZINC-FINGER, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, DNA-binding, Metal-binding, Nucleus, Phosphoprotein ;; 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.

3db3__assembly_1__model_1

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

Download this curve (.dat)

3db3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3db3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.52 Å
Rg (electron density)	16.67 Å
Total Rg	17.59 Å
Atom count	1164
Residues	139
Excluded volume	20549 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3db3__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 (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase UHRF1
Molecular weight formula_weight	19011.5 kDa
EC 编号 ec_number	6.3.2.-
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	1237

GMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGE

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	Trimethylated histone H3-K9 peptide
Molecular weight formula_weight	706.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TARKST

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3db3A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3db3A02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	99.622 Å
Unit-cell length b length_b	99.622 Å
Unit-cell length c length_c	41.232 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 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	31.770 Å
R factor r_factor	0.2151
R_work r_work	0.2119
R_free r_free	0.2820

Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide

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

E3 ubiquitin-protein ligase UHRF1

State in the Current Structure

Other States of the Same Protein in the Database

Trimethylated histone H3-K9 peptide

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

3db3__assembly_1__model_1

3db3__assembly_1__model_1 | I(q)

3db3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide

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

E3 ubiquitin-protein ligase UHRF1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Trimethylated histone H3-K9 peptide

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

3db3__assembly_1__model_1

3db3__assembly_1__model_1 | I(q)

3db3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)