9DQ3

Crystal structure of engineered Ipilimumab (mipi.4) Fab in complex with human CTLA-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.268 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Engineered ipilimumab variants that bind human and mouse CTLA-4.

Robison, B.Diong, S.J.Kumar, A.Moon, T.M.Chang, O.Chau, B.Bee, C.Barman, I.Rajpal, A.Korman, A.J.West, S.Strop, P.Lee, P.S.

(2025) MAbs 17: 2451296-2451296

  • DOI: https://doi.org/10.1080/19420862.2025.2451296
  • Primary Citation of Related Structures:  
    9DQ3, 9DQ4, 9DQ5

  • PubMed Abstract: 

    Testing of candidate monoclonal antibody therapeutics in preclinical models is an essential step in drug development. Identification of antibody therapeutic candidates that bind their human targets and cross-react to mouse orthologs is often challenging, especially for targets with low sequence homology. In such cases, surrogate antibodies that bind mouse orthologs must be used. The antibody 9D9, which binds mouse CTLA-4, is a commonly used surrogate for CTLA-4 checkpoint blockade studies in mouse cancer models. In this work, we reveal that 9D9 has significant biophysical dissimilarities to therapeutic CTLA-4 antibodies. The 9D9-mCTLA4 complex crystal structure was determined and shows that the surrogate antibody binds an epitope distinct from ipilimumab and tremelimumab. In addition, while ipilimumab has pH-independent binding to hCTLA-4, 9D9 loses binding to mCTLA-4 at physiologically relevant acidic pH ranges. We used phage and yeast display to engineer ipilimumab to bind mouse CTLA-4 with single-digit nM affinity from an initial state with no apparent binding. The engineered variants showed pH-independent and cross-reactive binding to both mouse and human CTLA-4. Crystal structures of a variant in complex with both mouse and human CTLA-4 confirmed that it targets an equivalent epitope as ipilimumab. These cross-reactive ipilimumab variants may facilitate improved translatability and future mechanism-of-action studies for anti-CTLA-4 targeting in murine models.


  • Organizational Affiliation

    Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytotoxic T-lymphocyte protein 4A [auth C]125Homo sapiensMutation(s): 0 
Gene Names: CTLA4CD152
UniProt & NIH Common Fund Data Resources
Find proteins for P16410 (Homo sapiens)
Explore P16410 
Go to UniProtKB:  P16410
PHAROS:  P16410
GTEx:  ENSG00000163599 
Entity Groups  
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UniProt GroupP16410
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mipi.4 heavy chainB [auth H]229Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
mipi.4 light chainC [auth L]215Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.268 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.023α = 90
b = 148.359β = 90
c = 48.439γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release