6UMX

Structural basis for specific inhibition of extracellular activation of pro/latent myostatin by SRK-015


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of specific inhibition of extracellular activation of pro- or latent myostatin by the monoclonal antibody SRK-015.

Dagbay, K.B.Treece, E.Streich Jr., F.C.Jackson, J.W.Faucette, R.R.Nikiforov, A.Lin, S.C.Boston, C.J.Nicholls, S.B.Capili, A.D.Carven, G.J.

(2020) J Biol Chem 295: 5404-5418

  • DOI: 10.1074/jbc.RA119.012293
  • Primary Citation of Related Structures:  
    6UMX

  • PubMed Abstract: 
  • Myostatin (or growth/differentiation factor 8 (GDF8)) is a member of the transforming growth factor β superfamily of growth factors and negatively regulates skeletal muscle growth. Its dysregulation is implicated in muscle wasting diseases. SRK-015 is a clinical-stage mAb that prevents extracellular proteolytic activation of pro- and latent myostatin ...

    Myostatin (or growth/differentiation factor 8 (GDF8)) is a member of the transforming growth factor β superfamily of growth factors and negatively regulates skeletal muscle growth. Its dysregulation is implicated in muscle wasting diseases. SRK-015 is a clinical-stage mAb that prevents extracellular proteolytic activation of pro- and latent myostatin. Here we used integrated structural and biochemical approaches to elucidate the molecular mechanism of antibody-mediated neutralization of pro-myostatin activation. The crystal structure of pro-myostatin in complex with 29H4-16 Fab, a high-affinity variant of SRK-015, at 2.79 Å resolution revealed that the antibody binds to a conformational epitope in the arm region of the prodomain distant from the proteolytic cleavage sites. This epitope is highly sequence-divergent, having only limited similarity to other closely related members of the transforming growth factor β superfamily. Hydrogen/deuterium exchange MS experiments indicated that antibody binding induces conformational changes in pro- and latent myostatin that span the arm region, the loops contiguous to the protease cleavage sites, and the latency-associated structural elements. Moreover, negative-stain EM with full-length antibodies disclosed a stable, ring-like antigen-antibody structure in which the two Fab arms of a single antibody occupy the two arm regions of the prodomain in the pro- and latent myostatin homodimers, suggesting a 1:1 (antibody:myostatin homodimer) binding stoichiometry. These results suggest that SRK-015 binding stabilizes the latent conformation and limits the accessibility of protease cleavage sites within the prodomain. These findings shed light on approaches that specifically block the extracellular activation of growth factors by targeting their precursor forms.


    Organizational Affiliation

    Scholar Rock Inc., Cambridge, Massachusetts 02139 gcarven@scholarrock.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Growth/differentiation factor 8A, F [auth B]365Homo sapiensMutation(s): 3 
Gene Names: MSTNGDF8
UniProt & NIH Common Fund Data Resources
Find proteins for O14793 (Homo sapiens)
Explore O14793 
Go to UniProtKB:  O14793
PHAROS:  O14793
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GL29H4-16 Fab Light Chain,GL29H4-16 Fab Light ChainB [auth L], D [auth l]215Homo sapiensMutation(s): 0 
Gene Names: IGLC2
UniProt & NIH Common Fund Data Resources
Find proteins for P0DOY2 (Homo sapiens)
Explore P0DOY2 
Go to UniProtKB:  P0DOY2
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GL29H4-16 Fab Heavy Chain,GL29H4-16 Fab Heavy ChainC [auth H], E [auth h]229Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q5EFE5 (Homo sapiens)
Explore Q5EFE5 
Go to UniProtKB:  Q5EFE5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth h]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.62α = 90
b = 110.01β = 90
c = 293.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2020-04-29
    Changes: Database references