7BXA

Crystal structure of PD-1 in complex with tislelizumab Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of PD-1 in complex with an antibody-drug tislelizumab used in tumor immune checkpoint therapy.

Lee, S.H.Lee, H.T.Lim, H.Kim, Y.Park, U.B.Heo, Y.S.

(2020) Biochem Biophys Res Commun 527: 226-231

  • DOI: 10.1016/j.bbrc.2020.04.121
  • Primary Citation of Related Structures:  
    7BXA

  • PubMed Abstract: 
  • Blocking of the interaction between Programmed cell death 1 (PD-1) and its ligand PD-L1 by monoclonal antibodies has elicited unprecedented therapeutic benefits and achieved a major breakthrough in immunotherapy of multiple types of tumors. Here, we determined the crystal structure of PD-1 in complex with the Fab fragment of tislelizumab ...

    Blocking of the interaction between Programmed cell death 1 (PD-1) and its ligand PD-L1 by monoclonal antibodies has elicited unprecedented therapeutic benefits and achieved a major breakthrough in immunotherapy of multiple types of tumors. Here, we determined the crystal structure of PD-1 in complex with the Fab fragment of tislelizumab. This monoclonal antibody was approved in December 2019 by the China National Medical Product Administration for Hodgkin's lymphoma and is under multiple clinical trials in China and the US. While the three complementarity determining regions (CDRs) in the light chain are involved in the target interaction, only CDR3 within the heavy chain interacts with PD-1. Tislelizumab binds the front β-sheet of PD-1 in a very similar way as PD-L1 binds to PD-1, thereby blocking the PD-1/PD-L1 interaction with a higher affinity. A comparative analysis of PD-1 interactions with therapeutic antibodies targeting PD-1 provides a better understanding of the blockade mechanism of PD-1/PD-L1 interaction in addition to useful information for the improvement of therapeutic antibodies capable of diminishing checkpoint signaling for cancer immunotherapy.


    Organizational Affiliation

    Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea. Electronic address: ysheo@konkuk.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Programmed cell death protein 1A, D [auth P]130Homo sapiensMutation(s): 1 
Gene Names: PDCD1PD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15116 (Homo sapiens)
Explore Q15116 
Go to UniProtKB:  Q15116
PHAROS:  Q15116
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
heavy chainB, E [auth H]230Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
light chainC, F [auth L]214Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.615α = 90
b = 73.081β = 90
c = 276.388γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release