5IUS

Crystal structure of human PD-L1 in complex with high affinity PD-1 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.889 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant.

Pascolutti, R.Sun, X.Kao, J.Maute, R.L.Ring, A.M.Bowman, G.R.Kruse, A.C.

(2016) Structure 24: 1719-1728

  • DOI: 10.1016/j.str.2016.06.026

  • PubMed Abstract: 
  • The immune checkpoint receptor PD-1 and its ligand, PD-L1, have emerged as key regulators of anti-tumor¬†immunity in humans. Recently, we reported an ultra-high-affinity PD-1 mutant, termed high-affinity consensus (HAC) PD-1, which shows superior ther ...

    The immune checkpoint receptor PD-1 and its ligand, PD-L1, have emerged as key regulators of anti-tumor immunity in humans. Recently, we reported an ultra-high-affinity PD-1 mutant, termed high-affinity consensus (HAC) PD-1, which shows superior therapeutic efficacy in mice compared with antibodies. However, the molecular details underlying the action of this agent remain incompletely understood, and a molecular view of PD-1/PD-L1 interactions in general is only beginning to emerge. Here, we report the structure of HAC PD-1 in complex with PD-L1, showing that it binds PD-L1 using a unique set of polar interactions. Biophysical studies and long-timescale molecular dynamics experiments reveal the mechanisms by which ten point mutations confer a 35,000-fold enhancement in binding affinity, and offer atomic-scale views of the role of conformational dynamics in PD-1/PD-L1 interactions. Finally, we show that the HAC PD-1 exhibits pH-dependent affinity, with pseudo-irreversible binding in a low pH setting akin to the tumor microenvironment.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death protein 1
A, B
129Homo sapiensMutation(s): 11 
Gene Names: PDCD1 (PD1)
Find proteins for Q15116 (Homo sapiens)
Go to Gene View: PDCD1
Go to UniProtKB:  Q15116
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death 1 ligand 1
C, D
225Homo sapiensMutation(s): 0 
Gene Names: CD274 (B7H1, PDCD1L1, PDCD1LG1, PDL1)
Find proteins for Q9NZQ7 (Homo sapiens)
Go to Gene View: CD274
Go to UniProtKB:  Q9NZQ7
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: 2.889 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 86.851α = 90.00
b = 86.851β = 90.00
c = 111.848γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited States1DP5OD021345

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations