5JDR

Structure of PD-L1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade.

Zhang, F.Wei, H.Wang, X.Bai, Y.Wang, P.Wu, J.Jiang, X.Wang, Y.Cai, H.Xu, T.Zhou, A.

(2017) Cell Discov 3: 17004-17004

  • DOI: 10.1038/celldisc.2017.4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The use of antibodies to target immune checkpoints, particularly PD-1/PD-L1, has made a profound impact in the field of cancer immunotherapy. Here, we identified KN035, an anti-PD-L1 nanobody that can strongly induce T-cell responses and inhibit tumo ...

    The use of antibodies to target immune checkpoints, particularly PD-1/PD-L1, has made a profound impact in the field of cancer immunotherapy. Here, we identified KN035, an anti-PD-L1 nanobody that can strongly induce T-cell responses and inhibit tumor growth. The crystal structures of KN035 complexed with PD-L1 and free PD-L1, solved here at 1.7 and 2.7 Å resolution, respectively, show that KN035 competes with PD-1 (programmed death protein 1) for the same flat surface on PD-L1, mainly through a single surface loop of 21 amino acids. This loop forms two short helices and develops key hydrophobic and ionic interactions with PD-L1 residues, such as Ile54, Tyr56 and Arg113, which are also involved in PD-1 binding. The detailed mutagenesis study identified the hotspot residues of the PD-L1 surface and provides an explanation for the stronger (~1 000-fold) binding of KN035 to PD-L1 than PD-1 and its lack of binding to PD-L2. Overall, this study reveals how a single immunoglobulin-variable scaffold of KN035 or PD-1 can bind to a flat protein surface through either a single surface loop or beta-sheet strands; and provides a basis for designing new immune checkpoint blockers and generating bi-specific antibodies for combination therapy.


    Organizational Affiliation

    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.,Alphamab Co. Ltd. , Suzhou, Jiangsu, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death 1 ligand 1
A, B
237Homo 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: 2.7 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 72.240α = 90.00
b = 91.510β = 90.00
c = 141.830γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-04-17 
  • Released Date: 2017-04-12 
  • Deposition Author(s): Zhou, A., Wei, H.

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release