3pz8

Crystal structure of Dvl1-DIX(Y17D) mutant

Method: X-RAY DIFFRACTION

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

Segment polarity protein dishevelled homolog DVL-1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DVL1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–106； UniProt 3–104 Author chain B； PDBConstruct 5–106； UniProt 3–104 Author chain C； PDBConstruct 5–106； UniProt 3–104 Author chain D； PDBConstruct 5–106； UniProt 3–104 Author chain E； PDBConstruct 5–106； UniProt 3–104 Author chain F； PDBConstruct 5–106； UniProt 3–104 Author chain G； PDBConstruct 5–106； UniProt 3–104 Author chain H； PDBConstruct 5–106； UniProt 3–104

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	3pz8
Deposition date deposition_date	2010-12-14
Structure title title	Crystal structure of Dvl1-DIX(Y17D) mutant
Keywords keywords	DIX domain, oligomerization, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

3pz8__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3pz8__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pz8__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	14.10 Å
Rg (electron density)	12.52 Å
Total Rg	13.91 Å
Atom count	671
Residues	83
Excluded volume	12065 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pz8__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pz8__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3pz8__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3pz8__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3pz8__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3pz8__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3pz8__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3pz8__assembly_8__model_1`	monomeric （1）	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 (2)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3pz8a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d3pz8b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d3pz8b2
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	d3pz8c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d3pz8d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d3pz8d2
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	d3pz8e1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d3pz8e2
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	d3pz8f1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d3pz8f2
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	d3pz8g_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d3pz8h_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3pz8A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3pz8B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3pz8C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3pz8D00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3pz8E00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3pz8F00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3pz8G00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	3pz8H00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily	130 —

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Unit-cell length a length_a	92.687 Å
Unit-cell length b length_b	106.780 Å
Unit-cell length c length_c	265.957 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	64

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.873 Å
Low-resolution limit resolution_low	41.015 Å
R factor r_factor	0.2316
R_work r_work	0.2298
R_free r_free	0.2646

Description description	Segment polarity protein dishevelled homolog DVL-1
Molecular weight formula_weight	11887.3 kDa
Mutation mutation	E3D, Y17D
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	5409

Crystal structure of Dvl1-DIX(Y17D) mutant

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

Segment polarity protein dishevelled homolog DVL-1

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

3pz8__assembly_4__model_1

3pz8__assembly_4__model_1 | I(q)

3pz8__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

Crystal structure of Dvl1-DIX(Y17D) mutant

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

Segment polarity protein dishevelled homolog DVL-1

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

3pz8__assembly_4__model_1

3pz8__assembly_4__model_1 | I(q)

3pz8__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)