SAXSdb — 4jvy

▼

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

Female germline-specific tumor suppressor gld-1

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 2 RNA 2	;RNA (5'-R(PCPUPAPAPCPAP*A)-3') ; × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLD1_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–196； UniProt 144–337 Author chain B； PDBConstruct 3–196； UniProt 144–337

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	4jvy
Deposition date deposition_date	2013-03-26
Structure title title	Structure of the STAR (signal transduction and activation of RNA) domain of GLD-1 bound to RNA
Keywords keywords	KH domain, STAR domain, RNA regulation, translational repression. RNA BINDING PROTEIN, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

4jvy__assembly_1__model_1

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

Download this curve (.dat)

4jvy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jvy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.30 Å
Rg (electron density)	32.05 Å
Total Rg	32.38 Å
Atom count	3346
Residues	395
Excluded volume	58720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jvy__assembly_1__model_1`	tetrameric （4）	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	Female germline-specific tumor suppressor gld-1
Molecular weight formula_weight	22479.9 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	3393

SHEATVEYLADLVKEKKHLTLFPHMFSNVERLLDDEIGRVRVALFQTEFPRVELPEPAGDMISITEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDKSKESAHRGKANWEHLEDDLHVLVQCEDTENRVHIKLQAALEQVKKLLIPAPEGTDELKRKQLMELAIINGTYRPMKSPNPAR

Source Source

Source organism organism	Caenorhabditis elegans
Common name common_name	nematode
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PCPUPAPAPCPAP*A)-3') ;
Molecular weight formula_weight	2188.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D,F

CUAACAA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4jvyA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	4jvyB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

▶

Unit-cell length a length_a	142.274 Å
Unit-cell length b length_b	142.274 Å
Unit-cell length c length_c	76.652 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.853 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	0.1797
R_work r_work	0.1752
R_free r_free	0.2220

Structure of the STAR (signal transduction and activation of RNA) domain of GLD-1 bound to RNA

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

Female germline-specific tumor suppressor gld-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

4jvy__assembly_1__model_1

4jvy__assembly_1__model_1 | I(q)

4jvy__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the STAR (signal transduction and activation of RNA) domain of GLD-1 bound to RNA

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

Female germline-specific tumor suppressor gld-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

4jvy__assembly_1__model_1

4jvy__assembly_1__model_1 | I(q)

4jvy__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)