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 5UTZ | pdb_00005utz

Human IL-2/Fab complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.247 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history. 

Literature

A human anti-IL-2 antibody that potentiates regulatory T cells by a structure-based mechanism.

Trotta, E., Bessette, P.H., Silveria, S.L., Ely, L.K., Jude, K.M., Le, D.T., Holst, C.R., Coyle, A., Potempa, M., Lanier, L.L., Garcia, K.C., Crellin, N.K., Rondon, I.J., Bluestone, J.A.

(2018) Nat Med 24: 1005-1014

  • DOI: https://doi.org/10.1038/s41591-018-0070-2
  • Primary Citation Related Structures: 
    5UTZ

  • PubMed Abstract: 

    Interleukin-2 (IL-2) has been shown to suppress immune pathologies by preferentially expanding regulatory T cells (T regs ). However, this therapy has been limited by off-target complications due to pathogenic cell expansion. Recent efforts have been focused on developing a more selective IL-2. It is well documented that certain anti-mouse IL-2 antibodies induce conformational changes that result in selective targeting of T regs . We report the generation of a fully human anti-IL-2 antibody, F5111.2, that stabilizes IL-2 in a conformation that results in the preferential STAT5 phosphorylation of T regs in vitro and selective expansion of T regs in vivo. When complexed with human IL-2, F5111.2 induced remission of type 1 diabetes in the NOD mouse model, reduced disease severity in a model of experimental autoimmune encephalomyelitis and protected mice against xenogeneic graft-versus-host disease. These results suggest that IL-2-F5111.2 may provide an immunotherapy to treat autoimmune diseases and graft-versus-host disease.


  • Organizational Affiliation: 
    • UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 249.7 kDa 
  • Atom Count: 17,641 
  • Modeled Residue Count: 2,251 
  • Deposited Residue Count: 2,292 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 5111 heavy chainA [auth H],
D [auth B],
G [auth F],
J
224Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6GMX6 (Homo sapiens)
Explore Q6GMX6 
Go to UniProtKB:  Q6GMX6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GMX6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 5111 light chainB [auth L],
E [auth C],
H [auth G],
K
216Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6IPQ0 (Homo sapiens)
Explore Q6IPQ0 
Go to UniProtKB:  Q6IPQ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IPQ0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-2C [auth D],
F [auth A],
I [auth E],
L [auth I]
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: 2.75 Å
  • R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.01α = 90
b = 145.73β = 95.38
c = 107.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI51321

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 2.0: 2019-12-11
    Changes: Author supporting evidence, Polymer sequence
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-11-13
    Changes: Structure summary