8EQ6 | pdb_00008eq6

PD1 signaling receptor bound to FAB Complex

• PDB DOI: https://doi.org/10.2210/pdb8EQ6/pdb

• Classification: SIGNALING PROTEIN/Immune System
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Expression vector pcDNA-inf
• Mutation(s): No 


• Deposited: 2022-10-07 Released: 2023-10-11 
• Deposition Author(s): Bjorkelid, C., Paluch, C., Robertson, N.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.257 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.225 (DCC) 

Starting Models: experimental

Literature

Antibody agonists trigger immune receptor signaling through local exclusion of receptor-type protein tyrosine phosphatases.

Lippert, A.H., Paluch, C., Gaglioni, M., Vuong, M.T., McColl, J., Jenkins, E., Fellermeyer, M., Clarke, J., Sharma, S., Moreira da Silva, S., Akkaya, B., Anzilotti, C., Morgan, S.H., Jessup, C.F., Korbel, M., Gileadi, U., Leitner, J., Knox, R., Chirifu, M., Huo, J., Yu, S., Ashman, N., Lui, Y., Wilkinson, I., Attfield, K.E., Fugger, L., Robertson, N.J., Lynch, C.J., Murray, L., Steinberger, P., Santos, A.M., Lee, S.F., Cornall, R.J., Klenerman, D., Davis, S.J.

(2024) Immunity 57: 256-270.e10

• PubMed: 38354703 
• DOI: https://doi.org/10.1016/j.immuni.2024.01.007
• Primary Citation Related Structures: 
  8EQ6, 9HK1


• PubMed Abstract: 
  

  Antibodies can block immune receptor engagement or trigger the receptor machinery to initiate signaling. We hypothesized that antibody agonists trigger signaling by sterically excluding large receptor-type protein tyrosine phosphatases (RPTPs) such as CD45 from sites of receptor engagement. An agonist targeting the costimulatory receptor CD28 produced signals that depended on antibody immobilization and were sensitive to the sizes of the receptor, the RPTPs, and the antibody itself. Although both the agonist and a non-agonistic anti-CD28 antibody locally excluded CD45, the agonistic antibody was more effective. An anti-PD-1 antibody that bound membrane proximally excluded CD45, triggered Src homology 2 domain-containing phosphatase 2 recruitment, and suppressed systemic lupus erythematosus and delayed-type hypersensitivity in experimental models. Paradoxically, nivolumab and pembrolizumab, anti-PD-1-blocking antibodies used clinically, also excluded CD45 and were agonistic in certain settings. Reducing these agonistic effects using antibody engineering improved PD-1 blockade. These findings establish a framework for developing new and improved therapies for autoimmunity and cancer.

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Organizational Affiliation: 
• Department of Chemistry, University of Cambridge, Cambridge, UK.
MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; MiroBio Ltd, Winchester House, Oxford Science Park, Oxford, UK.
MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
MiroBio Ltd, Winchester House, Oxford Science Park, Oxford, UK.
MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK.
Division of Immune Receptors and T cell Activation, Institute of Immunology, Medical University of Vienna, Vienna, Austria.
Absolute Antibody Ltd, Redcar, Cleveland, UK.
MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK; Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK.
MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK. Electronic address: [e-mail].
Department of Chemistry, University of Cambridge, Cambridge, UK. Electronic address: [e-mail].
MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 62.3 kDa 
• Atom Count: 4,117 
• Modeled Residue Count: 503 
• Deposited Residue Count: 571 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A	129	Homo sapiens	Mutation(s): 0  Gene Names: PDCD1, PD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15116 (Homo sapiens) Explore Q15116  Go to UniProtKB:  Q15116
PHAROS:  Q15116 GTEx:  ENSG00000188389

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody FAB light chain	B [auth L]	215	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody FAB heavy chain	C [auth H]	227	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.257 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.225 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.744	α = 90
b = 78.51	β = 106.423
c = 102.021	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Bjorkelid, C., Paluch, C., Robertson, N.J.

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Funding Organization	Location	Grant Number
Not funded	United Kingdom	na

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Structure summary
• Version 2.0: 2025-01-22
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary