Paired immunoglobulin-like receptor B (PirB) or Leukocyte immunoglobulin-like receptor subfamily B member 3 (LILRB3) full extracellular domain

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

Starting Models: experimental
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This is version 2.1 of the entry. See complete history


Structure and flexibility of the extracellular region of the PirB receptor.

Vlieg, H.C.Huizinga, E.G.Janssen, B.J.C.

(2019) J Biol Chem 294: 4634-4643

  • DOI: https://doi.org/10.1074/jbc.RA118.004396
  • Primary Citation of Related Structures:  
    6GRQ, 6GRS, 6GRT

  • PubMed Abstract: 

    Murine paired immunoglobulin receptor B (PirB) and its human ortholog leukocyte immunoglobulin-like receptor B2 (LILRB2) are widely expressed inhibitory receptors that interact with a diverse set of extracellular ligands and exert functions ranging from down-regulation of immune responses to inhibition of neuronal growth. However, structural information that could shed light on how PirB interacts with its ligands is lacking. Here, we report crystal structures of the PirB ectodomain; the first full ectodomain structure for a LILR family member, at 3.3-4.5 Å resolution. The structures reveal that PirB's six Ig-like domains are arranged at acute angles, similar to the structures of leukocyte immunoglobulin-like receptor (LILR) and killer-cell immunoglobulin-like receptor (KIR). We observe that this regular arrangement is followed throughout the ectodomain, resulting in an extended zigzag conformation. In two out of the five structures reported here, the repeating zigzag is broken by the first domain that can adopt two alternative orientations. Quantitative binding experiments revealed a 9 μm dissociation constant for PirB-myelin-associated glycoprotein (MAG) ectodomain interactions. Taken together, these structural findings and the observed PirB-MAG interactions are compatible with a model for intercellular signaling in which the PirB extracellular domains, which point away from the cell surface, enable interaction with ligands in trans .

  • Organizational Affiliation

    From Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Paired immunoglobulin-like receptor B606Mus musculusMutation(s): 0 
Gene Names: PirbLilrb3
Find proteins for Q8K4V6 (Mus musculus)
Explore Q8K4V6 
Go to UniProtKB:  Q8K4V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K4V6
Glycosylation Sites: 2
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.375α = 90
b = 106.375β = 90
c = 217.98γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific ResearchNetherlands723.012.002

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary