6SVL

human Myeloid-derived growth factor (MYDGF) in complex with neutralizing Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and receptor-interacting residues of MYDGF - a protein mediating ischemic tissue repair.

Ebenhoch, R.Akhdar, A.Reboll, M.R.Korf-Klingebiel, M.Gupta, P.Armstrong, J.Huang, Y.Frego, L.Rybina, I.Miglietta, J.Pekcec, A.Wollert, K.C.Nar, H.

(2019) Nat Commun 10: 5379-5379

  • DOI: 10.1038/s41467-019-13343-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Myeloid-derived growth factor (MYDGF) is a paracrine-acting protein that is produced by bone marrow-derived monocytes and macrophages to protect and repair the heart after myocardial infarction (MI). This effect can be used for the development of pro ...

    Myeloid-derived growth factor (MYDGF) is a paracrine-acting protein that is produced by bone marrow-derived monocytes and macrophages to protect and repair the heart after myocardial infarction (MI). This effect can be used for the development of protein-based therapies for ischemic tissue repair, also beyond the sole application in heart tissue. Here, we report the X-ray structure of MYDGF and identify its functionally relevant receptor binding epitope. MYDGF consists of a 10-stranded β-sandwich with a folding topology showing no similarities to other cytokines or growth factors. By characterizing the epitope of a neutralizing antibody and utilizing functional assays to study the activity of surface patch-mutations, we were able to localize the receptor interaction interface to a region around two surface tyrosine residues 71 and 73 and an adjacent prominent loop structure of residues 97-101. These findings enable structure-guided protein engineering to develop modified MYDGF variants with potentially improved properties for clinical use.


    Organizational Affiliation

    Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany. herbert.nar@boehringer-ingelheim.com.,Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT, 06877, USA.,Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany.,Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab_heavy_chain
A, D, G, H, K, O
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab_light_chain
B, E, I, L, M, P
234N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Myeloid-derived growth factor
C, F, J, N, Q, R
142Homo sapiensMutation(s): 0 
Gene Names: MYDGF (C19orf10)
Find proteins for Q969H8 (Homo sapiens)
Go to Gene View: MYDGF
Go to UniProtKB:  Q969H8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
E, M, R
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 89.519α = 71.54
b = 107.430β = 86.25
c = 109.369γ = 73.38
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-09-18 
  • Released Date: 2019-11-27 
  • Deposition Author(s): Ebenhoch, R., Nar, H.

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Database references