SAXSdb — 5nt7

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

ATP-dependent RNA helicase vasa, isoform A

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Maternal effect protein oskar × 2 （P25158） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VASA1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 3–163； UniProt 463–623 Author chain D； PDBConstruct 3–163； UniProt 463–623

Maternal effect protein oskar

Drosophila melanogaster

UniProt P25158

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	ATP-dependent RNA helicase vasa, isoform A × 2 （P09052） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OSKA_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 6–107； UniProt 139–240 Author chain C； PDBConstruct 6–107； UniProt 139–240

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	5nt7
Deposition date deposition_date	2017-04-27
Structure title title	Structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa
Keywords keywords	;DEAD-box RNA helicase, ATPase, RNA binding, regulator, stimulator, germ plasm, nuage, LOTUS, hydrolase- hydrolase regulator complex, hydrolase-hydrolase regulator complex ;; hydrolase/hydrolase regulator
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.

5nt7__assembly_1__model_1

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

Download this curve (.dat)

5nt7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nt7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.40 Å
Rg (electron density)	31.66 Å
Total Rg	31.97 Å
Atom count	3837
Residues	490
Excluded volume	68405 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nt7__assembly_1__model_1`	tetrameric （4）	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	ATP-dependent RNA helicase vasa, isoform A
Molecular weight formula_weight	18247.7 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	4466

GHSDVKQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRTC

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Maternal effect protein oskar
Molecular weight formula_weight	11917.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPLGSMTIIESNYISVREEYPDIDSEVRAILLSHAQNGITISSIKSEYRKLTGNPFPLHDNVTDFLLTIPNVTAECSESGKRIFNLKASLKNGHLLDMVLNQKERTS

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	613

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5nt7b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d5nt7d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5nt7A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	610 — LOTUS domain-like

Domain ID domain_id	5nt7B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5nt7C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	610 — LOTUS domain-like

Domain ID domain_id	5nt7D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	38.950 Å
Unit-cell length b length_b	39.040 Å
Unit-cell length c length_c	97.480 Å
Unit-cell angle α angle_alpha	89.28 °
Unit-cell angle β angle_beta	91.85 °
Unit-cell angle γ angle_gamma	99.26 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	48.713 Å
R factor r_factor	0.1696
R_work r_work	0.1690
R_free r_free	0.1991

Structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa

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

ATP-dependent RNA helicase vasa, isoform A

State in the Current Structure

Other States of the Same Protein in the Database

Maternal effect protein oskar

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

5nt7__assembly_1__model_1

5nt7__assembly_1__model_1 | I(q)

5nt7__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa

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

ATP-dependent RNA helicase vasa, isoform A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Maternal effect protein oskar

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

5nt7__assembly_1__model_1

5nt7__assembly_1__model_1 | I(q)

5nt7__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)