Biological Assembly 1  

 3D View: Structure | Electron Density

Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 143.12 kDa 
• Atom Count: 8421 
• Modelled Residue Count: 1086 
• Deposited Residue Count: 1302 
• Unique protein chains: 3

3NFP

Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain

• DOI: 10.2210/pdb3NFP/pdb

• Classification: Immune system/Cytokine
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-06-10 Released: 2010-09-15 
• Deposition Author(s): Yang, H., Wang, J., Du, J., Zhong, C., Guo, Y., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.301 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 

Literature

Structural basis of immunosuppression by the therapeutic antibody daclizumab

Yang, H., Wang, J., Du, J., Zhong, C., Zhang, D., Guo, H., Guo, Y., Ding, J.

(2010) Cell Res 20: 1361-1371

• PubMed: 20820193 
• DOI: 10.1038/cr.2010.130
• Primary Citation of Related Structures:  
  3NFS, 3NFP


• PubMed Abstract: 
  

Interleukin-2 (IL)-2 signaling plays a pivotal role in the activation of immune responses, and drugs that block this pathway have been shown to be effective for the immunosuppression in patients with organ transplantation to alleviate/eliminate allograft rejection. The first humanized monoclonal antibody (mAb) daclizumab falls into this category and shows high specificity and affinity against a key component of the IL-2 receptor complex, namely IL-2Rα. To reveal the molecular mechanism of the inhibition of the IL-2 signaling pathway by daclizumab, we determined the crystal structures of the daclizumab Fab in free form and in complex with the IL-2Rα ectodomain at 2.6 and 2.8 Å resolution, respectively. The daclizumab Fab adopts a similar conformation in the presence or absence of the IL-2Rα ectodomain. The antigen-binding site of daclizumab is mainly composed of five complementarity determining regions (CDRs) that form a large positively charged surface depression and two flanking patches that are generally hydrophobic. The conformational epitope consists of several discontinuous segments of the IL-2Rα ectodomain, a large portion of which overlaps with the regions that interact with IL-2, suggesting that the binding of daclizumab to IL-2Rα would prevent the IL-2 binding to IL-2Rα and the subsequent formation of the IL-2/IL-2Rαβγ(c) complex, and therefore block the IL-2 signaling pathway. These results also have implications for the design and development of improved mAb drugs targeting IL-2Rα.

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Organizational Affiliation: 

State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab fragment of daclizumab	A, C [auth H]	216	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab fragment of daclizumab	B, D [auth L]	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2 receptor subunit alpha	E [auth I], F [auth K]	223	Homo sapiens	Mutation(s): 0  Gene Names: IL2RA
UniProt & NIH Common Fund Data Resources
Find proteins for P01589 (Homo sapiens) Explore P01589  Go to UniProtKB:  P01589
PHAROS:  P01589 GTEx:  ENSG00000134460

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.301 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.167	α = 90
b = 114.973	β = 90
c = 247.555	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-10 
• Released Date: 2010-09-15 
Deposition Author(s): Yang, H., Wang, J., Du, J., Zhong, C., Guo, Y., Ding, J.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-10-16
  Changes: Database references, Derived calculations