6TXZ

FAB PART OF M6903 IN COMPLEX WITH HUMAN TIM3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification and characterization of M6903, an antagonistic anti-TIM-3 monoclonal antibody.

Zhang, D.Jiang, F.Zaynagetdinov, R.Huang, H.Sood, V.D.Wang, H.Zhao, X.Jenkins, M.H.Ji, Q.Wang, Y.Nannemann, D.P.Musil, D.Wesolowski, J.Paoletti, A.Bartholomew, T.Derner, M.G.An, Q.Iffland, C.Halle, J.P.

(2020) Oncoimmunology 9: 1744921-1744921

  • DOI: https://doi.org/10.1080/2162402X.2020.1744921
  • Primary Citation of Related Structures:  
    6TXZ

  • PubMed Abstract: 

    T cell immunoglobulin and mucin domain-3 (TIM-3) is an immune checkpoint that regulates normal immune responses but can be exploited by tumor cells to evade immune surveillance. TIM-3 is primarily expressed on immune cells, particularly on dysfunctional and exhausted T cells, and engagement of TIM-3 with its ligands promotes TIM-3-mediated T cell inhibition. Antagonistic ligand-blocking anti-TIM-3 antibodies have the potential to abrogate T cell inhibition, activate antigen-specific T cells, and enhance anti-tumor immunity. Here we describe M6903, a fully human anti-TIM-3 antibody without effector function and with high affinity and selectivity to TIM-3. We demonstrate that M6903 blocks the binding of TIM-3 to three of its ligands, phosphatidylserine (PtdSer), carcinoembryonic antigen cell adhesion-related molecule 1 (CEACAM1), and galectin 9 (Gal-9). These results are supported by an atomic resolution crystal structure and functional assays, which demonstrate that M6903 monotherapy enhanced T cell activation. This activation was further enhanced by the combination of M6903 with bintrafusp alfa, a bifunctional fusion protein that simultaneously blocks the transforming growth factor-β (TGF-β) and programmed death ligand 1 (PD-L1) pathways. M6903 and bintrafusp alfa combination therapy also enhanced anti-tumor efficacy in huTIM-3 knock-in mice, relative to either monotherapy. These in vitro and in vivo data, along with favorable pharmacokinetics in marmoset monkeys, suggest that M6903 as a monotherapy warrants further pre-clinical assessment and that M6903 and bintrafusp alfa may be a promising combination therapy in the clinic.


  • Organizational Affiliation

    Department of Immuno-Oncology, EMD Serono Research and Development Institute, Billerica, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatitis A virus cellular receptor 2
A, B, C, D
110Homo sapiensMutation(s): 0 
Gene Names: HAVCR2TIM3TIMD3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDQ0 (Homo sapiens)
Explore Q8TDQ0 
Go to UniProtKB:  Q8TDQ0
PHAROS:  Q8TDQ0
GTEx:  ENSG00000135077 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDQ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab HE [auth H],
F [auth I],
G [auth J],
H [auth K]
229Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab LI [auth L],
J [auth M],
K [auth N],
L [auth O]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.35α = 90
b = 270.115β = 90
c = 197.889γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description