1WAQ

Crystal structure of human Growth and Differentiation Factor 5 (GDF-5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Single Residue of Gdf-5 Defines Binding Specificity to Bmp Receptor Ib.

Nickel, J.Kotzsch, A.Sebald, W.Mueller, T.D.

(2005) J.Mol.Biol. 349: 933

  • DOI: 10.1016/j.jmb.2005.04.015

  • PubMed Abstract: 
  • Growth and differentiation factor 5 (GDF-5), a member of the TGF-beta superfamily, is involved in many developmental processes, like chondrogenesis and joint formation. Mutations in GDF-5 lead to diseases, e.g. chondrodysplasias like Hunter-Thompson, ...

    Growth and differentiation factor 5 (GDF-5), a member of the TGF-beta superfamily, is involved in many developmental processes, like chondrogenesis and joint formation. Mutations in GDF-5 lead to diseases, e.g. chondrodysplasias like Hunter-Thompson, Grebe and DuPan syndromes and brachydactyly. Similar to other TGF-beta superfamily members, GDF-5 transmits signals through binding to two different types of membrane-bound serine-/threonine-kinase receptors termed type I and type II. In contrast to the large number of ligands, only seven type I and five type II receptors have been identified to date, implicating a limited promiscuity in ligand-receptor interaction. However, in contrast to other members of the TGF-beta superfamily, GDF-5 shows a pronounced specificity in type I receptor interaction in cross-link experiments binding only to BMP receptor IB (BMPR-IB). In mice, deletion of either GDF-5 or BMPR-IB results in a similar phenotype, indicating that GDF-5 signaling is highly dependent on BMPR-IB. Here, we demonstrate by biosensor analysis that GDF-5 also binds to BMP receptor IA (BMPR-IA) but with approximately 12-fold lower affinity. Structural and mutational analyses revealed a single residue of GDF-5, Arg57 located in the pre-helix loop, being solely responsible for the high binding specificity to BMPR-IB. In contrast to wild-type GDF-5, variant GDF-5R57A interacts with BMPR-IA and BMPR-IB with a comparable high binding affinity. These results provide important insights into how receptor-binding specificity is generated at the molecular level and might be useful for the generation of receptor subtype specific activators or inhibitors.


    Related Citations: 
    • Molecular Recognition of Bmp-2 and Bmp Receptor Ia
      Keller, S.,Nickel, J.,Sebald, W.,Mueller, T.D.
      (2004) Nat.Struct.Mol.Biol. 11: 481


    Organizational Affiliation

    Lehrstuhl für Physiologische Chemie II, Theodor-Boveri Institut für Biowissenschaften (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GROWTH/DIFFERENTIATION FACTOR 5
A
117Homo sapiensMutation(s): 0 
Gene Names: GDF5 (BMP14, CDMP1)
Find proteins for P43026 (Homo sapiens)
Go to Gene View: GDF5
Go to UniProtKB:  P43026
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.771α = 90.00
b = 97.771β = 90.00
c = 43.325γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance