Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 36065.95 
• Atom Count: 2474 
• Residue Count: 319 
• Unique protein chains: 2

3BP5

Crystal structure of the mouse PD-1 and PD-L2 complex

• DOI: 10.2210/pdb3BP5/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2007-12-18 Released: 2008-07-15 
• Deposition Author(s): Yan, Q., Lazar-Molnar, E., Cao, E., Ramagopal, U.A., Toro, R., Nathenson, S.G., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.228 
• R-Value Work: 0.190 

Literature

Crystal structure of the complex between programmed death-1 (PD-1) and its ligand PD-L2.

Lazar-Molnar, E., Yan, Q., Cao, E., Ramagopal, U., Nathenson, S.G., Almo, S.C.

(2008) Proc.Natl.Acad.Sci.Usa 105: 10483-10488

• PubMed: 18641123 
• DOI: 10.1073/pnas.0804453105
• Primary Citation of Related Structures:  
  3BOV


• PubMed Abstract: 
  

Programmed death-1 (PD-1) is a member of the CD28/B7 superfamily that delivers negative signals upon interaction with its two ligands, PD-L1 or PD-L2. The high-resolution crystal structure of the complex formed by the complete ectodomains of murine PD-1 and PD-L2 revealed a 1:1 receptor:ligand stoichiometry and displayed a binding interface and overall molecular organization distinct from that observed in the CTLA-4/B7 inhibitory complexes. Furthermore, our structure also provides insights into the association between PD-1 and PD-L1 and highlights differences in the interfaces formed by the two PD-1 ligands (PD-Ls) Mutagenesis studies confirmed the details of the proposed PD-1/PD-L binding interfaces and allowed for the design of a mutant PD-1 receptor with enhanced affinity. These studies define spatial and organizational constraints that control the localization and signaling of PD-1/PD-L complexes within the immunological synapse and provide a basis for manipulating the PD-1 pathways for immunotherapy.

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Organizational Affiliation: 

Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Programmed cell death protein 1	A	117	Mus musculus	Mutation(s): 1  Gene Names: Pdcd1 (Pd1)
Find proteins for Q02242 (Mus musculus) Go to UniProtKB:  Q02242

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Programmed cell death 1 ligand 2	B	202	Mus musculus	Mutation(s): 0  Gene Names: Pdcd1lg2 (B7dc, Btdc, Cd273, Pdl2)
Find proteins for Q9WUL5 (Mus musculus) Go to UniProtKB:  Q9WUL5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.228 
• R-Value Work: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 43.933	α = 90.00
b = 84.056	β = 107.88
c = 52.108	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	data scaling
CBASS	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-18 
• Released Date: 2008-07-15 
• Deposition Author(s): Yan, Q., Lazar-Molnar, E., Cao, E., Ramagopal, U.A., Toro, R., Nathenson, S.G., Almo, S.C.

Revision History 

• Version 1.0: 2008-07-15
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Type: Refinement description