Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.38 kDa 
• Atom Count: 2604 
• Residue Count: 320 
• Unique protein chains: 2

3URF

Human RANKL/OPG complex

• DOI: 10.2210/pdb3URF/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-11-22 Released: 2012-07-11 
• Deposition Author(s): Wang, X.Q., Luan, X.D., Lu, Q.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.251 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

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

• PubMed: 22664871 
• DOI: 10.4049/jimmunol.1103387
• Primary Citation of Related Structures:  
  3URF


• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 11, soluble form	A	162	Homo sapiens	Mutation(s): 0  Gene Names: TNFSF11, OPGL, RANKL, TRANCE
Find proteins for O14788 (Homo sapiens) Explore O14788  Go to UniProtKB:  O14788
NIH Common Fund Data Resources
PHAROS:  O14788 GTEx:  ENSG00000120659

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 11B	Z	171	Homo sapiens	Mutation(s): 0  Gene Names: TNFRSF11B, OCIF, OPG
Find proteins for O00300 (Homo sapiens) Explore O00300  Go to UniProtKB:  O00300
NIH Common Fund Data Resources
PHAROS:  O00300 GTEx:  ENSG00000164761

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	Z	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.251 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.8	α = 90
b = 144.8	β = 90
c = 144.8	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-22 
• Released Date: 2012-07-11 
Deposition Author(s): Wang, X.Q., Luan, X.D., Lu, Q.Y.

Revision History 

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary