SAXSdb — 3ddt

▼

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

E3 ubiquitin-protein ligase TRIM63

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRI63_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–48； UniProt 117–161 Author chain B； PDBConstruct 4–48； UniProt 117–161 Author chain C； PDBConstruct 4–48； UniProt 117–161

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	3ddt
Deposition date deposition_date	2008-06-06
Structure title title	Crystal structure of the B2 box from MuRF1 in dimeric state
Keywords keywords	;zinc-binding motif, RING-like fold, Coiled coil, Cytoplasm, Ligase, Metal-binding, Muscle protein, Nucleus, Polymorphism, Ubl conjugation pathway, Zinc, Zinc-finger ;; LIGASE
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.

3ddt__assembly_1__model_1

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

Download this curve (.dat)

3ddt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ddt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	13.95 Å
Rg (electron density)	12.97 Å
Total Rg	14.11 Å
Atom count	718
Residues	95
Excluded volume	12908 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ddt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ddt__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase TRIM63
Molecular weight formula_weight	5277.2 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1215

GAMGSHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQS

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3ddta1
Class class	g — Small proteins
Fold Fold fold	g.43 — B-box zinc-binding domain
Superfamily Superfamily superfamily	g.43.1 — B-box zinc-binding domain
Family Family family	g.43.1.1 — B-box zinc-binding domain

Domain ID domain_id	d3ddta2
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	d3ddtb1
Class class	g — Small proteins
Fold Fold fold	g.43 — B-box zinc-binding domain
Superfamily Superfamily superfamily	g.43.1 — B-box zinc-binding domain
Family Family family	g.43.1.1 — B-box zinc-binding domain

Domain ID domain_id	d3ddtb2
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	d3ddtc_
Class class	g — Small proteins
Fold Fold fold	g.43 — B-box zinc-binding domain
Superfamily Superfamily superfamily	g.43.1 — B-box zinc-binding domain
Family Family family	g.43.1.1 — B-box zinc-binding domain

CATH v4.4 (3 domains)

Domain ID domain_id	3ddtA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	3ddtB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	3ddtC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

▶

Unit-cell length a length_a	76.220 Å
Unit-cell length b length_b	76.220 Å
Unit-cell length c length_c	146.930 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	36

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	17.694 Å
R factor r_factor	0.2010
R_work r_work	0.1990
R_free r_free	0.2519

Crystal structure of the B2 box from MuRF1 in dimeric state

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

E3 ubiquitin-protein ligase TRIM63

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

3ddt__assembly_1__model_1

3ddt__assembly_1__model_1 | I(q)

3ddt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of the B2 box from MuRF1 in dimeric state

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

E3 ubiquitin-protein ligase TRIM63

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

3ddt__assembly_1__model_1

3ddt__assembly_1__model_1 | I(q)

3ddt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)