5BNQ

Crystal structure of hRANKL-mRANK complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1038/srep14150
  • Primary Citation of Related Structures:  
    5BNQ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor ligand superfamily member 11160Homo sapiensMutation(s): 0 
Gene Names: TNFSF11OPGLRANKLTRANCE
UniProt & NIH Common Fund Data Resources
Find proteins for O14788 (Homo sapiens)
Explore O14788 
Go to UniProtKB:  O14788
PHAROS:  O14788
GTEx:  ENSG00000120659 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14788
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 11AB [auth R]216Mus musculusMutation(s): 0 
Gene Names: Tnfrsf11aRank
UniProt
Find proteins for O35305 (Mus musculus)
Explore O35305 
Go to UniProtKB:  O35305
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35305
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
I [auth R],
J [auth R],
K [auth R]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth R],
N [auth R],
O [auth R]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth R]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.188α = 90
b = 122.188β = 90
c = 94.473γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary