7DR4 | pdb_00007dr4

Complex of anti-human IL-2 antibody and human IL-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7DR4

This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human interleukin-2 in complex with TCB2, a new antibody-drug candidate with antitumor activity.

Kim, J.Lee, J.Y.Park, S.Y.Lee, Y.J.Kim, M.S.

(2021) Oncoimmunology 10: 1899671-1899671

  • DOI: https://doi.org/10.1080/2162402X.2021.1899671
  • Primary Citation Related Structures: 
    7DR4

  • PubMed Abstract: 

    Immunotherapy via interleukin-2 (IL-2) mediated activation of anti-tumor immune response is a promising approach for cancer treatment. The multi-potent cytokine, IL-2 has a central role in immune cell activation and homeostasis. Since IL-2 preferentially activates immunosuppressive T regulatory cells by IL-2Rα dependent manner, blocking IL-2:IL-2Rα interaction is a key to amplify the IL-2 activity in effector T cells toward anti-tumor response. Anti-IL-2 monoclonal antibodies are good candidates to control the IL-2:IL-2Rα interaction. In a previous study, we developed a new IL-2Rα mimetic antibody, TCB2, and showed that the human IL-2(hIL-2):TCB2 complex can stimulate T effector cells specifically and elicit potent anti-cancer immunotherapeutic effect, especially when administered in combination with immune checkpoint inhibitors. To understand the molecular mechanism, we determined the crystal structure of TCB2-Fab in a complex with hIL-2 at 2.5 Å resolution. Our structural analysis reveals that TCB2 binds to the central area of the hIL-2Rα binding region on hIL-2, and binding angle and epitope are different from previously known hIL-2Rα mimicking antibody NARA1 which recognizes the top part of hIL-2. TCB2 binding to hIL-2 also induces an allosteric effect that increases the affinity for the hetero-dimeric hIL-2 receptor, IL-2R(β + γ), on effector T cells.


  • Organizational Affiliation
    • Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 252.25 kDa 
  • Atom Count: 17,347 
  • Modeled Residue Count: 2,174 
  • Deposited Residue Count: 2,284 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-human IL-2 antibody, mouse Ig G, heavy chainA [auth H],
C [auth A],
E [auth C],
G [auth E]
224Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-human IL-2 antibody, mouse Ig G, kappa chainB [auth L],
D [auth B],
F [auth D],
H [auth F]
214Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-2I [auth G],
J [auth I],
K [auth J],
L [auth K]
133Homo sapiensMutation(s): 0 
Gene Names: IL2
UniProt & NIH Common Fund Data Resources
Find proteins for P60568 (Homo sapiens)
Explore P60568 
Go to UniProtKB:  P60568
PHAROS:  P60568
GTEx:  ENSG00000109471 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60568
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.334α = 90
b = 72.261β = 92.711
c = 210.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary