SAXSdb — 3v69

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

Protein Filia

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–124 Chain B； UniProt 1–124	Fragment：UNP RESIDUES 1-124	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, 2.0M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.20 Å R-free 0.273

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3V69	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
12DL Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs Deposited 2026-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain LA 1–440（440 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
24MC Structure of oocyte cytoplasmic lattices Deposited 2026-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain O 1–346（346 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9SFP Native cytoplasmic lattices from mouse oocytes Deposited 2025-08-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric	Chain C 1–440（440 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
9W2M Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte Deposited 2025-07-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain D 1–128（128 aa） Chain d 1–128（128 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9XRL Structure of mouse cytoplasmic lattice (CPL) repeating unit Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 73 PDB declaration: 73-meric	Chain 4 1–440（440 aa） Chain 6 1–440（440 aa） Chain AA 1–440（440 aa）	Not recorded	ZN ZINC ION × 13 GTP GUANOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 6.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FILIA_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–140； UniProt 1–124 Author chain B； PDBConstruct 17–140； 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	3v69
Deposition date deposition_date	2011-12-19
Structure title title	Filia-N crystal structure
Keywords keywords	FILIA, RNA-binding, embryogenesis, KH domain, RNA binding, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.51 Å
Radius of gyration Rg (electron density) rg_electron	18.40 Å
Forward intensity I(0) i0	12229200.00
Molecular weight molecular_weight	27006.0 kDa
Excluded volume excluded_volume	34268 Å³
Envelope volume envelope_volume	40416 Å³
Hydration-shell volume shell_volume	18420 Å³
Envelope diameter envelope_diameter	65.8 Å
Shell Rg shell_rg	24.47 Å
Envelope Rg envelope_rg	18.78 Å
Shape Rg shape_rg	18.41 Å
Total Rg total_rg	19.37 Å
Total atoms total_atoms	1903
Residues n_residues	228
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	63.4 Å
Rg (real space) rg_real	19.45 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.2230e+07
I(0) uncertainty (real space) i0_real_error	1.5350e+05
Rg (reciprocal space) rg_reciprocal	19.46 Å
I(0) (reciprocal space) i0_reciprocal	12230000.0000
Solution quality estimate total_estimate	0.8068
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.300
Kurtosis Kurtosis kurtosis	-0.280
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3633000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3v69A00
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	3v69B00
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

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8. Citations (1)

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Unit-cell length a length_a	38.296 Å
Unit-cell length b length_b	73.962 Å
Unit-cell length c length_c	89.961 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	2.200 Å
Low-resolution limit resolution_low	28.566 Å
R factor r_factor	0.2081
R_work r_work	0.2046
R_free r_free	0.2726

Description description	Protein Filia
Molecular weight formula_weight	16675.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2031

Filia-N crystal structure

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

Protein Filia

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

fit	/app/data/saxs_computation/v6/3v69/3v69.fit
pddf	/app/data/pr_computation/v6/3v69/3v69.pr.out
profile	/app/data/saxs_computation/v6/3v69/3v69.dat