5BNQ

Crystal structure of hRANKL-mRANK complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A RANKL mutant used as an inter-species vaccine for efficient immunotherapy of osteoporosis.

Liu, C.Zhao, Y.He, W.Wang, W.Chen, Y.Zhang, S.Ma, Y.Gohda, J.Ishida, T.Walter, T.S.Owens, R.J.Stuart, D.I.Ren, J.Gao, B.

(2015) Sci Rep 5: 14150-14150

  • DOI: 10.1038/srep14150

  • PubMed Abstract: 
  • Anti-cytokine therapeutic antibodies have been demonstrated to be effective in the treatment of several auto-immune disorders. However, The problems in antibody manufacture and the immunogenicity caused by multiple doses of antibodies inspire people ...

    Anti-cytokine therapeutic antibodies have been demonstrated to be effective in the treatment of several auto-immune disorders. However, The problems in antibody manufacture and the immunogenicity caused by multiple doses of antibodies inspire people to use auto-cytokine as immunogen to induce anti-cytokine antibodies. Nevertheless, the tolerance for inducing immune response against self-antigen has hindered the wide application of the strategy. To overcome the tolerance, here we proposed a strategy using the inter-species cytokine as immunogen for active immunization (TISCAI) to induce anti-cytokine antibody. As a proof of concept, an inter-species cytokine RANKL was successfully used as immunogen to induce anti-RANKL immune response. Furthermore, to prevent undesirable side-effects, the human RANKL was mutated based on the crystal structure of the complex of human RANKL and its rodent counterpart receptor RANK. We found, the antibodies produced blocked the osteoclast development in vitro and osteoporosis in OVX rat models. The results demonstrated this strategy adopted is very useful for general anti-cytokine immunotherapy for different diseases settings.


    Organizational Affiliation

    Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, NO.16, Dongzhimennei South Street, Dongcheng District, Beijing 100700, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor ligand superfamily member 11
A
160Homo 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 11A
R
216Mus musculusMutation(s): 0 
Gene Names: Tnfrsf11a (Rank)
Find proteins for O35305 (Mus musculus)
Go to UniProtKB:  O35305
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, R
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
R
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, R
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 122.188α = 90.00
b = 122.188β = 90.00
c = 94.473γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-05-26 
  • Released Date: 2015-10-14 
  • Deposition Author(s): Ren, J.

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release