Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.94 kDa 
• Atom Count: 4696 
• Residue Count: 569 
• Unique protein chains: 4

2DYP

Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G

• DOI: 10.2210/pdb2DYP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-15 Released: 2006-11-07 
• Deposition Author(s): Shiroishi, M., Kuroki, K., Rasubala, L., Kohda, D., Maenaka, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.278 
• R-Value Work: 0.233 

Literature

Structural basis for recognition of the nonclassical MHC molecule HLA-G by the leukocyte Ig-like receptor B2 (LILRB2/LIR2/ILT4/CD85d)

Shiroishi, M., Kuroki, K., Rasubala, L., Tsumoto, K., Kumagai, I., Kurimoto, E., Kato, K., Kohda, D., Maenaka, K.

(2006) Proc Natl Acad Sci U S A 103: 16412-16417

• PubMed: 17056715 
• DOI: 10.1073/pnas.0605228103
• Primary Citation of Related Structures:  
  2DYP


• PubMed Abstract: 
  

HLA-G is a nonclassical MHC class I (MHCI) molecule that can suppress a wide range of immune responses in the maternal-fetal interface. The human inhibitory immune receptors leukocyte Ig-like receptor (LILR) B1 [also called LIR1, Ig-like transcript 2 (ILT2), or CD85j] and LILRB2 (LIR2/ILT4/CD85d) preferentially recognize HLA-G. HLA-G inherently exhibits various forms, including beta(2)-microglobulin (beta(2)m)-free and disulfide-linked dimer forms. Notably, LILRB1 cannot recognize the beta(2)m-free form of HLA-G or HLA-B27, but LILRB2 can recognize the beta(2)m-free form of HLA-B27. To date, the structural basis for HLA-G/LILR recognition remains to be examined. Here, we report the 2.5-A resolution crystal structure of the LILRB2/HLA-G complex. LILRB2 exhibits an overlapping but distinct MHCI recognition mode compared with LILRB1 and dominantly recognizes the hydrophobic site of the HLA-G alpha3 domain. NMR binding studies also confirmed these LILR recognition differences on both conformed (heavy chain/peptide/beta(2)m) and free forms of beta(2)m. Binding studies using beta(2)m-free MHCIs revealed differential beta(2)m-dependent LILR-binding specificities. These results suggest that subtle structural differences between LILRB family members cause the distinct binding specificities to various forms of HLA-G and other MHCIs, which may in turn regulate immune suppression.

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Organizational Affiliation: 

Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, alpha chain G	A	277	Homo sapiens	Mutation(s): 1  Gene Names: HLA-G, HLA-6.0, HLAG
Find proteins for P17693 (Homo sapiens) Explore P17693  Go to UniProtKB:  P17693
NIH Common Fund Data Resources
PHAROS  P17693 GTEx  ENSG00000204632

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
9 Mer Peptide From Histone H2A.x	C	9	N/A	Mutation(s): 0
Find proteins for P16104 (Homo sapiens) Explore P16104  Go to UniProtKB:  P16104
NIH Common Fund Data Resources
PHAROS  P16104 GTEx  ENSG00000188486

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte immunoglobulin-like receptor subfamily B member 2	D	196	Homo sapiens	Mutation(s): 0  Gene Names: LILRB2, ILT4, LIR2, MIR10
Find proteins for Q8N423 (Homo sapiens) Explore Q8N423  Go to UniProtKB:  Q8N423
NIH Common Fund Data Resources
PHAROS  Q8N423 GTEx  ENSG00000131042

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.278 
• R-Value Work: 0.233 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.4	α = 90
b = 81.4	β = 90
c = 186.733	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-09-15 
• Released Date: 2006-11-07 
Deposition Author(s): Shiroishi, M., Kuroki, K., Rasubala, L., Kohda, D., Maenaka, K.

Revision History 

• Version 1.0: 2006-11-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance