6TXZ | pdb_00006txz

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 (Depositor) 
  • R-Value Work: 
    0.197 (Depositor) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6TXZ

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 236.81 kDa 
  • Atom Count: 16,053 
  • Modeled Residue Count: 2,134 
  • Deposited Residue Count: 2,212 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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:|  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 
Find similar proteins by:|  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 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free:  0.253 (Depositor) 
  • R-Value Work:  0.197 (Depositor) 
  • R-Value Observed: 0.197 (Depositor) 
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
  • Version 1.3: 2024-11-13
    Changes: Structure summary