1NPU

CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MURINE PD-1

• PDB DOI: https://doi.org/10.2210/pdb1NPU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-01-20 Released: 2004-03-23 
• Deposition Author(s): Zhang, X., Schwartz, J.-C.D., Guo, X., Cao, E., Chen, L., Zhang, Z.-Y., Nathenson, S.G., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Structural and functional analysis of the costimulatory receptor programmed death-1.

Zhang, X., Schwartz, J.C., Guo, X., Bhatia, S., Cao, E., Lorenz, M., Cammer, M., Chen, L., Zhang, Z.Y., Edidin, M.A., Nathenson, S.G., Almo, S.C.

(2004) Immunity 20: 337-347

• PubMed: 15030777 
• DOI: https://doi.org/10.1016/s1074-7613(04)00051-2
• Primary Citation of Related Structures:  
  1NPU


• PubMed Abstract: 
  

  PD-1, a member of the CD28/CTLA-4/ICOS costimulatory receptor family, delivers negative signals that have profound effects on T and B cell immunity. The 2.0 A crystal structure of the extracellular domain of murine PD-1 reveals an Ig V-type topology with overall similarity to the CTLA-4 monomer; however, there are notable differences in regions relevant to function. Our structural and biophysical data show that PD-1 is monomeric both in solution as well as on cell surface, in contrast to CTLA-4 and other family members that are all disulfide-linked homodimers. Furthermore, our structure-based mutagenesis studies identify the ligand binding surface of PD-1, which displays significant differences compared to those present in the other members of the family.

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Organizational Affiliation: 

Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.18 kDa 
• Atom Count: 979 
• Modelled Residue Count: 116 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A	117	Mus musculus	Mutation(s): 1  Gene Names: PDCD1 OR PD1
UniProt
Find proteins for Q02242 (Mus musculus) Explore Q02242  Go to UniProtKB:  Q02242

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.965	α = 90
b = 50.802	β = 90
c = 75.278	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-23 
Deposition Author(s): Zhang, X., Schwartz, J.-C.D., Guo, X., Cao, E., Chen, L., Zhang, Z.-Y., Nathenson, S.G., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Structure summary
• Version 1.4: 2021-10-27
  Changes: Database references
• Version 1.5: 2023-08-16
  Changes: Data collection, Refinement description
• Version 1.6: 2024-10-30
  Changes: Structure summary