SAXSdb — 3sek

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

Growth/differentiation factor 8

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 268–376	Fragment：UNP Residues 268-376	Follistatin-related protein 3 × 2 （O95633） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 7.5；293 K；potassium thiocyanate, PEG 3350, pH 7.5, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.270

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 3SEK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3HH2 Crystal structure of the myostatin:follistatin 288 complex Deposited 2009-05-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 268–376（109 aa） Fragment：UNP residues 268-376 Chain B 268–376（109 aa） Fragment：UNP residues 268-376	Not recorded	PO4 PHOSPHATE ION × 3 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；PEG 1000, Ethanol, Phosphate/citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.15 Å R-free 0.249
5JI1 Crystal Structure of GDF8 Deposited 2016-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 268–376（109 aa） Fragment：UNP residues 268-376 Chain B 268–376（109 aa） Fragment：UNP residues 268-376	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM 2-(N-morpholino)ethanesulfonic acid pH 6.0, 40% 2-Methyl-2,4-pentanediol	Resolution 2.25 Å R-free 0.277

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GDF8_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–109； UniProt 268–376

Follistatin-related protein 3

Homo sapiens

UniProt O95633

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 36–244	Fragment：UNP Residues 36-244	Growth/differentiation factor 8 × 2 （O08689） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：hanging drop；pH 7.5；293 K；potassium thiocyanate, PEG 3350, pH 7.5, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.270

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 3SEK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KCX Solution NMR Structure of Kazal-1 Domain of Human Follistatin-related protein 3 (FSTL-3). Northeast Structural Genomics Target HR6186A. Deposited 2008-12-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 97–169（73 aa） Fragment：Kazal-1 domain, residues 97-169	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] FSTL-3-1, 20 mM MES-2, 200 mM sodium chloride-3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2 mM [U-100% 15N] FSTL-3-4, 20 mM MES-5, 200 mM sodium chloride-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3B4V X-Ray structure of Activin in complex with FSTL3 Deposited 2007-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 27–263（237 aa） Chain D 27–263（237 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 3350, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.48 Å R-free 0.279
3B4V X-Ray structure of Activin in complex with FSTL3 Deposited 2007-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 27–263（237 aa） Chain H 27–263（237 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 3350, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.48 Å R-free 0.279

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FSTL3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–209； UniProt 36–244

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	3sek
Deposition date deposition_date	2011-06-10
Structure title title	Crystal Structure of the Myostatin:Follistatin-like 3 Complex
Keywords keywords	;protein-protein complex, TB domain, cystine knot motif, TGF-beta fold, disulfide linked dimer, follistatin domain (FSD), signaling protein ;; SIGNALING PROTEIN
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	26.14 Å
Radius of gyration Rg (electron density) rg_electron	25.73 Å
Forward intensity I(0) i0	23101500.00
Molecular weight molecular_weight	33761.0 kDa
Excluded volume excluded_volume	41017 Å³
Envelope volume envelope_volume	56139 Å³
Hydration-shell volume shell_volume	19676 Å³
Envelope diameter envelope_diameter	96.0 Å
Shell Rg shell_rg	30.65 Å
Envelope Rg envelope_rg	25.71 Å
Shape Rg shape_rg	25.75 Å
Total Rg total_rg	26.26 Å
Total atoms total_atoms	2338
Residues n_residues	310
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	89.6 Å
Rg (real space) rg_real	26.31 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	2.3100e+07
I(0) uncertainty (real space) i0_real_error	3.3090e+05
Rg (reciprocal space) rg_reciprocal	26.26 Å
I(0) (reciprocal space) i0_reciprocal	23100000.0000
Solution quality estimate total_estimate	0.8548
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.418
Kurtosis Kurtosis kurtosis	-0.523
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1755000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.723; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Growth/differentiation factor 8
Molecular weight formula_weight	12422.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	2403

DFGLDCDEHSTESRCCRYPLTVDFEAFGWDWIIAPKRYKANYCSGECEFVFLQKYPHTHLVHQANPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS

来源 Source

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	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Follistatin-related protein 3
Molecular weight formula_weight	22233.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GVCWLQQGQEATCSLVLQTDVTRAECCASGNIDTAWSNLTHPGNKINLLGFLGLVHCLPCKDSCDGVECGPGKACRMLGGRPRCECAPDCSGLPARLQVCGSDGATYRDECELRAARCRGHPDLSVMYRGRCRKSCEHVVCPRPQSCVVDQTGSAHCVVCRAAPCPVPSSPGQELCGNNNVTYISSCHMRQATCFLGRSIGVRHAGSCA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	59

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3sekb_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3sekB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	3sekC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	290 — Extracellular Matrix Fibrillin
Homologous superfamily homologous superfamily	10 — TGF-beta binding (TB) domain

Domain ID domain_id	3sekC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3sekC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	82.086 Å
Unit-cell length b length_b	82.086 Å
Unit-cell length c length_c	312.691 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 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.401 Å
Low-resolution limit resolution_low	35.540 Å
R factor r_factor	0.2469
R_work r_work	0.2457
R_free r_free	0.2703

fit	/app/data/saxs_computation/se/3sek/3sek.fit
pddf	/app/data/pr_computation/se/3sek/3sek.pr.out
profile	/app/data/saxs_computation/se/3sek/3sek.dat

Crystal Structure of the Myostatin:Follistatin-like 3 Complex

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

Growth/differentiation factor 8

State in the Current Structure

Other States of the Same Protein in the Database

Follistatin-related protein 3

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)