5XXY

Crystal structure of PD-L1 complexed with atezolizumab fab at 2.9A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab.

Zhang, F.Qi, X.Wang, X.Wei, D.Wu, J.Feng, L.Cai, H.Wang, Y.Zeng, N.Xu, T.Zhou, A.Zheng, Y.

(2017) Oncotarget 8: 90215-90224

  • DOI: 10.18632/oncotarget.21652

  • PubMed Abstract: 
  • Monoclonal antibodies targeting PD-1/PD-L1 signaling pathway have achieved unprecedented success in cancer treatment over the last few years. Atezolizumab is the first PD-L1 monoclonal antibody approved by US FDA for cancer therapy; however the molec ...

    Monoclonal antibodies targeting PD-1/PD-L1 signaling pathway have achieved unprecedented success in cancer treatment over the last few years. Atezolizumab is the first PD-L1 monoclonal antibody approved by US FDA for cancer therapy; however the molecular basis of atezolizumab in blocking PD-1/PD-L1 interaction is not fully understood. Here we have solved the crystal structure of PD-L1/atezolizumab complex at 2.9 angstrom resolution. The structure shows that atezolizumab binds the front beta-sheet of PD-L1 through three CDR loops from the heavy chain and one CDR loop from the light chain. The binding involves extensive hydrogen-bonding and hydrophobic interactions. Notably there are multiple aromatic residues from the CDR loops forming Pi-Pi stacking or cation-Pi interactions within the center of the binding interface and the buried surface area is more than 2000 Å 2 , which is the largest amongst all the known PD-L1/antibody structures. Mutagenesis study revealed that two hot-spot residues (E58, R113) of PD-L1 contribute significantly to the binding of atezolizumab. The structure also shows that atezolizumab binds PD-L1 with a distinct heavy and light chain orientation and it blocks PD-1/PD-L1 interaction through competing with PD-1 for the same PD-L1 surface area. Taken together, the complex structure of PD-L1/atezolizumab solved here revealed the molecular mechanism of atezolizumab in immunotherapy and provides basis for future monoclonal antibody optimization and rational design of small chemical compounds targeting PD-L1 surface.


    Organizational Affiliation

    The Therapeutic Antibody Research Center of SEU-Alphamab, Southeast University, Nanjing, China.,Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of The Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Faculty of Basic Medicine, Nanjing Medical University, Nanjing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
heavy chain of atezolizumab fab
H
240N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
light chain of atezolizumab fab
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death 1 ligand 1
A
124Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 127.220α = 90.00
b = 72.710β = 104.44
c = 63.800γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-07-05 
  • Released Date: 2017-09-20 
  • Deposition Author(s): Zhou, A., Zhang, F.

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references, Structure summary
  • Version 1.2: 2018-04-11
    Type: Data collection, Database references