3URF

Human RANKL/OPG complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of Human RANKL Complexed with Its Decoy Receptor Osteoprotegerin

Luan, X.D.Lu, Q.Y.Jiang, Y.N.Zhang, S.Y.Wang, Q.Yuan, H.H.Zhao, W.M.Wang, J.W.Wang, X.Q.

(2012) J.Immunol. 189: 245-252

  • DOI: 10.4049/jimmunol.1103387

  • PubMed Abstract: 
  • Receptor activator of NF-κB ligand (RANKL), its signaling receptor RANK, and its decoy receptor osteoprotegerin (OPG) constitute a molecular triad that is critical in regulating bone remodeling, and also plays multiple roles in the immune system. OPG ...

    Receptor activator of NF-κB ligand (RANKL), its signaling receptor RANK, and its decoy receptor osteoprotegerin (OPG) constitute a molecular triad that is critical in regulating bone remodeling, and also plays multiple roles in the immune system. OPG binds RANKL directly to block its interaction with RANK. In this article, we report the 2.7-Å crystal structure of human RANKL trimer in complex with the N-terminal fragment of human OPG containing four cysteine-rich TNFR homologous domains (OPG-CRD). The structure shows that RANKL trimer uses three equivalent grooves between two neighboring monomers to interact with three OPG-CRD monomers symmetrically. A loop from the CRD3 domain of OPG-CRD inserts into the shallow groove of RANKL, providing the major binding determinant that is further confirmed by affinity measurement and osteoclast differentiation assay. These results, together with a previously reported mouse RANKL/RANK complex structure, reveal that OPG exerts its decoy receptor function by directly blocking the accessibilities of important interacting residues of RANKL for RANK recognition. Structural comparison with TRAIL/death receptor 5 complex also reveals structural basis for the cross-reactivity of OPG to TRAIL.


    Organizational Affiliation

    Center for Structural Biology, School of Life Sciences, Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor ligand superfamily member 11, soluble form
A
162Homo sapiensMutation(s): 0 
Gene Names: TNFSF11 (OPGL, RANKL, TRANCE)
Find proteins for O14788 (Homo sapiens)
Go to Gene View: TNFSF11
Go to UniProtKB:  O14788
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 11B
Z
171Homo sapiensMutation(s): 0 
Gene Names: TNFRSF11B (OCIF, OPG)
Find proteins for O00300 (Homo sapiens)
Go to Gene View: TNFRSF11B
Go to UniProtKB:  O00300
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
Z
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 144.800α = 90.00
b = 144.800β = 90.00
c = 144.800γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
ADSCdata collection
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release