SAXSdb — 4v31

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

CEREBLON ISOFORM 4

MAGNETOSPIRILLUM GRYPHISWALDENSE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 2'-DEOXYURIDINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 2'-DEOXYURIDINE × 1 CITRATE ANION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 2'-DEOXYURIDINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4TVL0_9PROT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–125； UniProt 1–124 Author chain B； PDBConstruct 2–125； UniProt 1–124 Author chain C； PDBConstruct 2–125； UniProt 1–124

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	4v31
Deposition date deposition_date	2014-10-15
Structure title title	Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine
Keywords keywords	SIGNALING PROTEIN, TERATOGENICITY, AROMATIC CAGE; 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.

4v31__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4v31__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4v31__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	14.33 Å
Rg (electron density)	12.90 Å
Total Rg	14.28 Å
Atom count	852
Residues	105
Excluded volume	14998 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4v31__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4v31__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4v31__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	CEREBLON ISOFORM 4
Molecular weight formula_weight	13703.6 kDa
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	2747

AMPLDAGGQNSTQMVLAPGASIFRCRQCGQTISRRDWLLPMGGDHEHVVFNPAGMIFRVWCFSLAQGLRLIGAPSGEFSWFKGYDWTIALCGQCGSHLGWHYEGGSQPQTFFGLIKDRLAEGPAD

Source Source

Source organism organism	MAGNETOSPIRILLUM GRYPHISWALDENSE
NCBI taxonomy ID ncbi_taxonomy_id	431944
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	3

Entity 3 Entity 3 non-polymer

Description description	2'-DEOXYURIDINE
Molecular weight formula_weight	228.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	164

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4v31A00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	20 — Peptide methionine sulfoxide reductase.

Domain ID domain_id	4v31B00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	20 — Peptide methionine sulfoxide reductase.

Domain ID domain_id	4v31C00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	20 — Peptide methionine sulfoxide reductase.

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Unit-cell length a length_a	56.809 Å
Unit-cell length b length_b	59.993 Å
Unit-cell length c length_c	88.370 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	37.410 Å
R factor r_factor	0.1666
R_work r_work	0.1639
R_free r_free	0.2185

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine

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

CEREBLON ISOFORM 4

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

4v31__assembly_2__model_1

4v31__assembly_2__model_1 | I(q)

4v31__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine

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

CEREBLON ISOFORM 4

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

4v31__assembly_2__model_1

4v31__assembly_2__model_1 | I(q)

4v31__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)