SAXSdb — 3f2o

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

SPRY domain-containing SOCS box protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	20-mer peptide from ATP-dependent RNA helicase vasa × 1 （P09052） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	20-mer peptide from ATP-dependent RNA helicase vasa × 1 （P09052） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPSB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–233； UniProt 24–233 Author chain B； PDBConstruct 24–233； UniProt 24–233

20-mer peptide from ATP-dependent RNA helicase vasa

OrganismNot specified

UniProt P09052

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SPRY domain-containing SOCS box protein 1 × 1 （Q96BD6） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SPRY domain-containing SOCS box protein 1 × 1 （Q96BD6） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VASA_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–20； UniProt 184–203 Author chain D； PDBConstruct 1–20； UniProt 184–203

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	3f2o
Deposition date deposition_date	2008-10-30
Structure title title	Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 1 (SPSB1) in complex with a 20-residue VASA peptide
Keywords keywords	;apoptosis, nucleus, transcription regulation, SGC, Structural Genomics Consortium, Phosphoprotein, Ubl conjugation pathway, ATP-binding, Developmental protein, Differentiation, Helicase, Hydrolase, Nucleotide-binding, Oogenesis, APOPTOSIS-HYDROLASE COMPLEX ;; APOPTOSIS/HYDROLASE
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.

3f2o__assembly_1__model_1

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

Download this curve (.dat)

3f2o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f2o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.82 Å
Rg (electron density)	16.62 Å
Total Rg	17.71 Å
Atom count	1754
Residues	221
Excluded volume	30916 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f2o__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3f2o__assembly_2__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	SPRY domain-containing SOCS box protein 1
Molecular weight formula_weight	26530.9 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	3777

MHHHHHHSSGVDLGTENLYFQSMQELQGLDYCKPTRLDLLLDMPPVSYDVQLLHSWNNNDRSLNVFVKEDDKLIFHRHPVAQSTDAIRGKVGYTRGLHVWQITWAMRQRGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRNRLYHDGKNQPSKTYPAFLEPDETFIVPDSFLVALDMDDGTLSFIVDGQYMGVAFRGLKGKKLYPVVSAVWGHCEIRMRYLNGLDPE

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 polymer

Description description	20-mer peptide from ATP-dependent RNA helicase vasa
Molecular weight formula_weight	2497.7 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

DINNNNNIVEDVERKREFYI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	287

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Unit-cell length a length_a	75.665 Å
Unit-cell length b length_b	80.654 Å
Unit-cell length c length_c	86.864 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	8

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

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	38.240 Å
R factor r_factor	0.1822
R_work r_work	0.1795
R_free r_free	0.2320

Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 1 (SPSB1) in complex with a 20-residue VASA peptide

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

SPRY domain-containing SOCS box protein 1

State in the Current Structure

Other States of the Same Protein in the Database

20-mer peptide from ATP-dependent RNA helicase vasa

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

3f2o__assembly_1__model_1

3f2o__assembly_1__model_1 | I(q)

3f2o__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)

Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 1 (SPSB1) in complex with a 20-residue VASA peptide

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

SPRY domain-containing SOCS box protein 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

20-mer peptide from ATP-dependent RNA helicase vasa

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

3f2o__assembly_1__model_1

3f2o__assembly_1__model_1 | I(q)

3f2o__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)