5X8L | pdb_00005x8l

PD-L1 in complex with atezolizumab


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp3.10 Å
  • R-Value Free:&nbsp
    0.256 (Depositor), 0.250 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.208 (Depositor), 0.210 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.210&nbsp(Depositor)&nbsp

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 1.1 of the entry. See complete&nbsphistory.&nbsp


Literature

Molecular mechanism of PD-1/PD-L1 blockade via anti-PD-L1 antibodies atezolizumab and durvalumab

Lee, H.T.,&nbspLee, J.Y.,&nbspLim, H.,&nbspLee, S.H.,&nbspMoon, Y.J.,&nbspPyo, H.J.,&nbspRyu, S.E.,&nbspShin, W.,&nbspHeo, Y.S.

(2017) Sci Rep&nbsp7: 5532-5532

  • DOI:&nbsphttps://doi.org/10.1038/s41598-017-06002-8
  • Primary Citation of Related Structures: &nbsp
    5X8L, 5X8M

  • PubMed Abstract:&nbsp

    In 2016 and 2017, monoclonal antibodies targeting PD-L1, including atezolizumab, durvalumab, and avelumab, were approved by the FDA for the treatment of multiple advanced cancers. And many other anti-PD-L1 antibodies are under clinical trials. Recently, the crystal structures of PD-L1 in complex with BMS-936559 and avelumab have been determined, revealing details of the antigen-antibody interactions. However, it is still unknown how atezolizumab and durvalumab specifically recognize PD-L1, although this is important for investigating novel binding sites on PD-L1 targeted by other therapeutic antibodies for the design and improvement of anti-PD-L1 agents. Here, we report the crystal structures of PD-L1 in complex with atezolizumab and durvalumab to elucidate the precise epitopes involved and the structural basis for PD-1/PD-L1 blockade by these antibodies. A comprehensive comparison of PD-L1 interactions with anti-PD-L1 antibodies provides a better understanding of the mechanism of PD-L1 blockade as well as new insights into the rational design of improved anti-PD-L1 therapeutics.


  • Organizational Affiliation:&nbsp

    Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Programmed cell death 1 ligand 1A,
D [auth B],
G [auth C],
J [auth D],
M [auth E]
123Homo sapiensMutation(s): 1&nbsp
Gene Names:&nbspCD274,&nbspB7H1,&nbspPDCD1L1,&nbspPDCD1LG1,&nbspPDL1
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspQ9NZQ7&nbsp(Homo sapiens)
Explore&nbspQ9NZQ7&nbsp
Go to UniProtKB: &nbspQ9NZQ7
PHAROS: &nbspQ9NZQ7
GTEx: &nbspENSG00000120217&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZQ7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
atezolizumab light chainB [auth K],
E [auth L],
H [auth M],
K [auth N],
N [auth O]
214Homo sapiensMutation(s): 0&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
atezolizumab heavy chainC [auth F],
F [auth G],
I [auth H],
L [auth S],
O [auth J]
230Homo sapiensMutation(s): 0&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp3.10 Å
  • R-Value Free:&nbsp 0.256 (Depositor), 0.250 (DCC)&nbsp
  • R-Value Work:&nbsp 0.208 (Depositor), 0.210 (DCC)&nbsp
  • R-Value Observed:&nbsp0.210&nbsp(Depositor)&nbsp
Space Group:&nbspP 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.197α = 90
b = 169.793β = 90
c = 206.098γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary