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5jhw

Crystal Structure of the GDF11:Follistatin 288 complex

Method: X-RAY DIFFRACTION Dmax: 105.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Growth/differentiation factor 11

Homo sapiens

UniProt O95390

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 A； UniProt 299–407 Chain B； UniProt 299–407 Fragment：UNP residues 299-407 Follistatin × 2 （P19883） PO4 PHOSPHATE ION × 3 FLC CITRATE ANION × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；100mM Phosphate/Citrate pH 4.2, 14% EtOH, 1% PEG 1000 Resolution 2.35 Å R-free 0.247

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 5JHW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5E4G Crystal structure of human growth differentiation factor 11 (GDF-11) Deposited 2015-10-06 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 299–407（109 aa） Fragment：UNP residues 299-407
Not recorded PG4 TETRAETHYLENE GLYCOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.18 M magnesium acetate, 0.1 M HEPES, pH 7.5, 22.5% PEG3350, 0.01 M strontium chloride
Resolution 1.50 Å R-free 0.207
5UHM Apo-Structure of Mature Growth Differentiation Factor 11 Deposited 2017-01-11 Different construct 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 299–407（109 aa）
Chain B 299–407（109 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.75；298.15 K；5mM Calcium Chloride 0.1M Sodium Acetate 33% MPD
Resolution 1.90 Å R-free 0.258
6MAC Ternary structure of GDF11 bound to ActRIIB-ECD and Alk5-ECD Deposited 2018-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 300–407（108 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；.05-.15M sodium acetate 12-24% polyethylene glycol 8000 .05-.15M sodium thiocyanate
Resolution 2.34 Å R-free 0.267
7MRZ Structure of GDF11 bound to fused ActRIIB-ECD and Alk4-ECD with Anti-ActRIIB Fab fragment Deposited 2021-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain A 299–407（109 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 0.9M ammonium sulfate, 0.9 M KCl
Resolution 3.00 Å R-free 0.327

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GDF11_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–109； UniProt 299–407 Author chain B； PDBConstruct 1–109； UniProt 299–407

Follistatin

Homo sapiens

UniProt P19883

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 30–317 Chain D； UniProt 30–317 Fragment：UNP residues 30-317 Growth/differentiation factor 11 × 2 （O95390） PO4 PHOSPHATE ION × 3 FLC CITRATE ANION × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；100mM Phosphate/Citrate pH 4.2, 14% EtOH, 1% PEG 1000 Resolution 2.35 Å R-free 0.247

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 5JHW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2B0U The Structure of the Follistatin:Activin Complex Deposited 2005-09-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 30–317（288 aa） Fragment：Follistatin-288
Chain D 30–317（288 aa） Fragment：Follistatin-288
Not recorded IR3 IRIDIUM (III) ION × 5 MLI MALONATE ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 3350, 200 mM Malonate, pH 7.0, vapor diffusion, hanging drop, temperature 295K
Resolution 2.80 Å R-free 0.297
2P6A The structure of the Activin:Follistatin 315 complex Deposited 2007-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 30–344（315 aa）
Chain D 30–344（315 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20-23% PEG 1000, 200mM MgCl2, 3% EtOH, 20mM Trimethyl-amine HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298 K
Resolution 3.40 Å R-free 0.324
3HH2 Crystal structure of the myostatin:follistatin 288 complex Deposited 2009-05-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 30–317（288 aa） Fragment：UNP residues 30-317
Chain D 30–317（288 aa） Fragment：UNP residues 30-317
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

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

View Construct and Data Evidence
UniProt name FST_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–288； UniProt 30–317 Author chain D； PDBConstruct 1–288； UniProt 30–317

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5jhw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5jhw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5jhw
Deposition date deposition_date2016-04-21
Structure title titleCrystal Structure of the GDF11:Follistatin 288 complex
Keywords keywordsGDF11, follistatin, TGFbeta, Ligand, CYTOKINE-Signaling Protein complex; CYTOKINE/Signaling Protein
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.50 Å
Radius of gyration Rg (electron density) rg_electron31.86 Å
Forward intensity I(0) i0146891000.00
Molecular weight molecular_weight88528.0 kDa
Excluded volume excluded_volume107390 ų
Envelope volume envelope_volume151230 ų
Hydration-shell volume shell_volume39554 ų
Envelope diameter envelope_diameter117.0 Å
Shell Rg shell_rg39.18 Å
Envelope Rg envelope_rg31.17 Å
Shape Rg shape_rg31.86 Å
Total Rg total_rg32.43 Å
Total atoms total_atoms6117
Residues n_residues784
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax105.6 Å
Rg (real space) rg_real32.44 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real1.4690e+08
I(0) uncertainty (real space) i0_real_error2.6120e+06
Rg (reciprocal space) rg_reciprocal32.47 Å
I(0) (reciprocal space) i0_reciprocal146900000.0000
Solution quality estimate total_estimate0.9022
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.8 Å
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.460
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12160000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.945
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5jhwa_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.0 — automated matches
Domain ID domain_idd5jhwb_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id5jhwC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology290 — Extracellular Matrix Fibrillin
Homologous superfamily homologous superfamily10 — TGF-beta binding (TB) domain
Domain ID domain_id5jhwC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5jhwC03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5jhwC04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5jhwD01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology290 — Extracellular Matrix Fibrillin
Homologous superfamily homologous superfamily10 — TGF-beta binding (TB) domain
Domain ID domain_id5jhwD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5jhwD03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5jhwD04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily30 —
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8. Citations (1)

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9. Files and Curves (10)