3ME2

Crystal structure of mouse RANKL-RANK complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Functional Insights of RANKL-RANK Interaction and Signaling.

Liu, C.Walter, T.S.Huang, P.Zhang, S.Zhu, X.Wu, Y.Wedderburn, L.R.Tang, P.Owens, R.J.Stuart, D.I.Ren, J.Gao, B.

(2010) J Immunol 

  • DOI: 10.4049/jimmunol.0904033
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bone remodeling involves bone resorption by osteoclasts and synthesis by osteoblasts and is tightly regulated by the receptor activator of the NF-kappaB ligand (RANKL)/receptor activator of the NF-kappaB (RANK)/osteoprotegerin molecular triad. RANKL, ...

    Bone remodeling involves bone resorption by osteoclasts and synthesis by osteoblasts and is tightly regulated by the receptor activator of the NF-kappaB ligand (RANKL)/receptor activator of the NF-kappaB (RANK)/osteoprotegerin molecular triad. RANKL, a member of the TNF superfamily, induces osteoclast differentiation, activation and survival upon interaction with its receptor RANK. The decoy receptor osteoprotegerin inhibits osteoclast formation by binding to RANKL. Imbalance in this molecular triad can result in diseases, including osteoporosis and rheumatoid arthritis. In this study, we report the crystal structures of unliganded RANK and its complex with RANKL and elucidation of critical residues for the function of the receptor pair. RANK represents the longest TNFR with four full cysteine-rich domains (CRDs) in which the CRD4 is stabilized by a sodium ion and a rigid linkage with CRD3. On association, RANK moves via a hinge region between the CRD2 and CRD3 to make close contact with RANKL; a significant structural change previously unseen in the engagement of TNFR superfamily 1A with its ligand. The high-affinity interaction between RANK and RANKL, maintained by continuous contact between the pair rather than the patched interaction commonly observed, is necessary for the function because a slightly reduced affinity induced by mutation produces significant disruption of osteoclast formation. The structures of RANK and RANKL-RANK complex and the biological data presented in the paper are essential for not only our understanding of the specific nature of the signaling mechanism and of disease-related mutations found in patients but also structure based drug design.


    Organizational Affiliation

    The Center for Molecular Immunology, Institute of Microbiology, Chinese Academy of Sciences, Department of Orthopaedics, Chinese People's Liberation Army General Hospital, Beijing, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor ligand superfamily member 11A171Mus musculusMutation(s): 0 
Gene Names: OpglRanklTnfsf11Trance
Find proteins for O35235 (Mus musculus)
Explore O35235 
Go to UniProtKB:  O35235
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 11AR216Mus musculusMutation(s): 0 
Gene Names: RankTnfrsf11a
Find proteins for O35305 (Mus musculus)
Explore O35305 
Go to UniProtKB:  O35305
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A, R
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
R
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.225α = 90
b = 121.225β = 90
c = 94.995γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance