5JI1

Crystal Structure of GDF8

• PDB DOI: https://doi.org/10.2210/pdb5JI1/pdb

• Classification: CYTOKINE
• Organism(s): Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2016-04-21 Released: 2017-03-22 
• Deposition Author(s): Walker, R.G., Thompson, T.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Muscular Dystrophy Association, American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.277 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 

Literature

Structural basis for potency differences between GDF8 and GDF11.

Walker, R.G., Czepnik, M., Goebel, E.J., McCoy, J.C., Vujic, A., Cho, M., Oh, J., Aykul, S., Walton, K.L., Schang, G., Bernard, D.J., Hinck, A.P., Harrison, C.A., Martinez-Hackert, E., Wagers, A.J., Lee, R.T., Thompson, T.B.

(2017) BMC Biol 15: 19-19

• PubMed: 28257634 
• DOI: https://doi.org/10.1186/s12915-017-0350-1
• Primary Citation of Related Structures:  
  5JHW, 5JI1, 5UHM


• PubMed Abstract: 
  

  Growth/differentiation factor 8 (GDF8) and GDF11 are two highly similar members of the transforming growth factor β (TGFβ) family. While GDF8 has been recognized as a negative regulator of muscle growth and differentiation, there are conflicting studies on the function of GDF11 and whether GDF11 has beneficial effects on age-related dysfunction. To address whether GDF8 and GDF11 are functionally identical, we compared their signaling and structural properties.

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Organizational Affiliation: 

Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH, 45267, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.67 kDa 
• Atom Count: 1,529 
• Modelled Residue Count: 187 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth/differentiation factor 8	A, B	109	Mus musculus	Mutation(s): 0  Gene Names: Mstn, Gdf8
UniProt
Find proteins for O08689 (Mus musculus) Explore O08689  Go to UniProtKB:  O08689

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.277 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.606	α = 90
b = 77.739	β = 90
c = 119.544	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Walker, R.G., Thompson, T.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM114640
Muscular Dystrophy Association	United States	240087
American Heart Association	United States	12PRE11790027

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description