SAXSdb — 3f8i

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

E3 ubiquitin-protein ligase UHRF1

Mus musculus

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(DCPDCPDAPDTPDGP(5CM)PDGPDCPDTPDGPDAPDC)-3' × 1 5'-D(DGPDTPDCPDAPDGPDCPDGPDCPDAPDTPDGPDG)-3' × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(DCPDCPDAPDTPDGP(5CM)PDGPDCPDTPDGPDAPDC)-3' × 1 5'-D(DGPDTPDCPDAPDGPDCPDGPDCPDAPDTPDGPDG)-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_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–212； UniProt 418–628 Author chain B； PDBConstruct 2–212； UniProt 418–628

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	3f8i
Deposition date deposition_date	2008-11-12
Structure title title	Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21
Keywords keywords	;UHRF1, base flipping, 5-methylcytosine, CpG methylation, Cell cycle, Developmental protein, DNA damage, DNA repair, DNA-binding, Ligase, Metal-binding, Nucleus, Phosphoprotein, Transcription, Transcription regulation, Ubl conjugation, Ubl conjugation pathway, Zinc, Zinc-finger, LIGASE-DNA COMPLEX ;; LIGASE/DNA
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.

3f8i__assembly_1__model_1

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

Download this curve (.dat)

3f8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f8i__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)	18.32 Å
Total Rg	19.23 Å
Atom count	2093
Residues	229
Excluded volume	35015 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f8i__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3f8i__assembly_2__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	23915.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4313

HMPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKDRTRQLGLTMQYPEGYLEALANKEKSRKR

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(DCPDCPDAPDTPDGP(5CM)PDGPDCPDTPDGPDAPDC)-3'
Molecular weight formula_weight	3637.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

CCATGCGCTGAC

Entity 3 Entity 3 polymer

Description description	5'-D(DGPDTPDCPDAPDGPDCPDGPDCPDAPDTPDGPDG)-3'
Molecular weight formula_weight	3703.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G

GTCAGCGCATGG

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3f8ia1
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	d3f8ia2
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	d3f8ib1
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	d3f8ib2
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 (2 domains)

Domain ID domain_id	3f8iA01
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	3f8iB01
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	50.084 Å
Unit-cell length b length_b	62.416 Å
Unit-cell length c length_c	113.447 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	34.530 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2680

Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21

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

3f8i__assembly_1__model_1

3f8i__assembly_1__model_1 | I(q)

3f8i__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21

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

3f8i__assembly_1__model_1

3f8i__assembly_1__model_1 | I(q)

3f8i__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (2)