SAXSdb — 3clz

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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–DNA	Monomer	Protein 1 DNA 2	5'-D(DGPDGPDGPDCPDCP(5CM)PDGPDCPDAPDGPDGPDG)-3' × 1 5'-D(DCPDCPDCPDTPDGPDCPDGPDGPDGPDCPDCPDC)-3' × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(DGPDGPDGPDCPDCP(5CM)PDGPDCPDAPDGPDGPDG)-3' × 1 5'-D(DCPDCPDCPDTPDGPDCPDGPDGPDGPDCPDCPDC)-3' × 1 water × 3	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(DGPDGPDGPDCPDCP(5CM)PDGPDCPDAPDGPDGPDG)-3' × 1 5'-D(DCPDCPDCPDTPDGPDCPDGPDGPDGPDCPDCPDC)-3' × 1 water × 3	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(DGPDGPDGPDCPDCP(5CM)PDGPDCPDAPDGPDGPDG)-3' × 1 5'-D(DCPDCPDCPDTPDGPDCPDGPDGPDGPDCPDCPDC)-3' × 1 water × 3	Consistent with all polymers

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 2–205； UniProt 414–617 Author chain B； PDBConstruct 2–205； UniProt 414–617 Author chain C； PDBConstruct 2–205； UniProt 414–617 Author chain D； PDBConstruct 2–205； UniProt 414–617

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	3clz
Deposition date deposition_date	2008-03-20
Structure title title	The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA
Keywords keywords	;CELL CYCLE, DNA DAMAGE, DNA REPAIR, DNA-BINDING, BASE FLIPPING, LIGASE, METAL BINDING, NUCLEASE, DNA REPLICATION, TRANSCRIPTIONAL SILENCING, CHROMATIN, PHOSPHORYLATION, TRANSCRIPTION, TRANSCRIPTION REGULATION, UBL CONJUGATION, UBL CONJUGATION PATHWAY, ZINC, ZINC-FINGER, STRUCTURAL GENOMICS CONSORTIUM, SGC, Metal-binding, Nucleus, Phosphoprotein, Polymorphism ;; 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.

3clz__assembly_1__model_1

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

Download this curve (.dat)

3clz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3clz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.34 Å
Rg (electron density)	18.42 Å
Total Rg	19.32 Å
Atom count	2085
Residues	227
Excluded volume	34934 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3clz__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3clz__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3clz__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3clz__assembly_4__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase UHRF1
Molecular weight formula_weight	23769.6 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,C,D
Atom count atom_count	9090

MPSNHYGPIPGIPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDHGNFFTYTGSGGRDLSGNKRTAEQSCDQKLTNTNRALALNCFAPINDQEGAEAKDWRSGKPVRVVRNVKGGKNSKYAPAEGNRYDGIYKVVKYWPEKGKSGFLVWRYLLRRDDDEPGPWTKEGKDRIKKLGLTMQYPEGYLEALANAHHHHHH

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	5'-D(DGPDGPDGPDCPDCP(5CM)PDGPDCPDAPDGPDGPDG)-3'
Molecular weight formula_weight	3743.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G,I,K

GGGCCCGCAGGG

Entity 3 Entity 3 polymer

Description description	5'-D(DCPDCPDCPDTPDGPDCPDGPDGPDGPDCPDCPDC)-3'
Molecular weight formula_weight	3600.3 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H,J,L

CCCTGCGGGCCC

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	640

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3clza2
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	d3clza3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3clzb2
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	d3clzb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3clzc2
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	d3clzc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3clzd2
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	d3clzd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3clzA01
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	3clzB01
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	3clzC01
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	3clzD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	280 — PUA domain-like
Homologous superfamily homologous superfamily	10 — SRA-YDG

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Unit-cell length a length_a	76.198 Å
Unit-cell length b length_b	111.359 Å
Unit-cell length c length_c	97.403 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	38.630 Å
R factor r_factor	0.1910
R_work r_work	0.1888
R_free r_free	0.2315

The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3clz__assembly_1__model_1

3clz__assembly_1__model_1 | I(q)

3clz__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 (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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3clz__assembly_1__model_1

3clz__assembly_1__model_1 | I(q)

3clz__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 (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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)