3QBQ

Crystal structure of extracellular domains of mouse RANK-RANKL complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based development of a receptor activator of nuclear factor-kappaB ligand (RANKL) inhibitor peptide and molecular basis for osteopetrosis

Ta, H.M.Nguyen, G.T.T.Jin, H.M.Choi, J.K.Park, H.Kim, N.S.Hwang, H.Y.Kim, K.K.

(2010) Proc.Natl.Acad.Sci.USA 107: 20281-20286

  • DOI: 10.1073/pnas.1011686107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The receptor activator of nuclear factor-κB (RANK) and its ligand RANKL, which belong to the tumor necrosis factor (TNF) receptor-ligand family, mediate osteoclastogenesis. The crystal structure of the RANKL ectodomain (eRANKL) in complex with the RA ...

    The receptor activator of nuclear factor-κB (RANK) and its ligand RANKL, which belong to the tumor necrosis factor (TNF) receptor-ligand family, mediate osteoclastogenesis. The crystal structure of the RANKL ectodomain (eRANKL) in complex with the RANK ectodomain (eRANK) combined with biochemical assays of RANK mutants indicated that three RANK loops (Loop1, Loop2, and Loop3) bind to the interface of a trimeric eRANKL. Loop3 is particularly notable in that it is structurally distinctive from other TNF-family receptors and forms extensive contacts with RANKL. The disulfide bond (C125-C127) at the tip of Loop3 is important for determining the unique topology of Loop3, and docking E126 close to RANKL, which was supported by the inability of C127A or E126A mutants of RANK to bind to RANKL. Inhibitory activity of RANK mutants, which contain loops of osteoprotegerin (OPG), a soluble decoy receptor to RANKL, confirmed that OPG shares the similar binding mode with RANK and OPG. Loop3 plays a key role in RANKL binding. Peptide inhibitors designed to mimic Loop3 blocked the RANKL-induced differentiation of osteoclast precursors, suggesting that they could be developed as therapeutic agents for the treatment of osteoporosis and bone-related diseases. Furthermore, some of the RANK mutations associated with autosomal recessive osteopetrosis (ARO) resulted in reduced RANKL-binding activity and failure to induce osteoclastogenesis. These results, together with structural interpretation of eRANK-eRANKL interaction, provided molecular understanding for pathogenesis of ARO.


    Organizational Affiliation

    Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor ligand superfamily member 11
A, C
160Mus musculusMutation(s): 0 
Gene Names: Tnfsf11 (Opgl, Rankl, Trance)
Find proteins for O35235 (Mus musculus)
Go to UniProtKB:  O35235
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 11A
B, D
170Mus musculusMutation(s): 0 
Gene Names: Tnfrsf11a (Rank)
Find proteins for O35305 (Mus musculus)
Go to UniProtKB:  O35305
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.227 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 120.860α = 90.00
b = 120.860β = 90.00
c = 93.425γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance