6UMU

Human apo PD-1 triple mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.183 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.

Tang, S.Kim, P.S.

(2019) Proc.Natl.Acad.Sci.USA 116: 24500-24506

  • DOI: 10.1073/pnas.1916916116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Immune checkpoint blockade of programmed death-1 (PD-1) by monoclonal antibody drugs has delivered breakthroughs in the treatment of cancer. Nonetheless, small-molecule PD-1 inhibitors could lead to increases in treatment efficacy, safety, and global ...

    Immune checkpoint blockade of programmed death-1 (PD-1) by monoclonal antibody drugs has delivered breakthroughs in the treatment of cancer. Nonetheless, small-molecule PD-1 inhibitors could lead to increases in treatment efficacy, safety, and global access. While the ligand-binding surface of apo-PD-1 is relatively flat, it harbors a striking pocket in the murine PD-1/PD-L2 structure. An analogous pocket in human PD-1 may serve as a small-molecule drug target, but the structure of the human complex is unknown. Because the CC' and FG loops in murine PD-1 adopt new conformations upon binding PD-L2, we hypothesized that mutations in these two loops could be coupled to pocket formation and alter PD-1's affinity for PD-L2. Here, we conducted deep mutational scanning in these loops and used yeast surface display to select for enhanced PD-L2 binding. A PD-1 variant with three substitutions binds PD-L2 with an affinity two orders of magnitude higher than that of the wild-type protein, permitting crystallization of the complex. We determined the X-ray crystal structures of the human triple-mutant PD-1/PD-L2 complex and the apo triple-mutant PD-1 variant at 2.0 Å and 1.2 Å resolution, respectively. Binding of PD-L2 is accompanied by formation of a prominent pocket in human PD-1, as well as substantial conformational changes in the CC' and FG loops. The structure of the apo triple-mutant PD-1 shows that the CC' loop adopts the ligand-bound conformation, providing support for allostery between the loop and pocket. This human PD-1/PD-L2 structure provide critical insights for the design and discovery of small-molecule PD-1 inhibitors.


    Organizational Affiliation

    Stanford ChEM-H, Stanford University, Stanford, CA 94305; kimpeter@stanford.edu.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305.,Stanford ChEM-H, Stanford University, Stanford, CA 94305.,Chan Zuckerberg Biohub, San Francisco, CA 94158.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death protein 1
A
129Homo sapiensMutation(s): 3 
Gene Names: PDCD1 (PD1)
Find proteins for Q15116 (Homo sapiens)
Go to Gene View: PDCD1
Go to UniProtKB:  Q15116
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.183 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.154 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 46.172α = 90.00
b = 46.172β = 90.00
c = 89.270γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-10-10 
  • Released Date: 2019-11-27 
  • Deposition Author(s): Tang, S., Kim, P.S.

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-18
    Type: Database references