Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.86 kDa 
• Atom Count: 6124 
• Residue Count: 747 
• Unique protein chains: 3

2D31

Crystal structure of disulfide-linked HLA-G dimer

• DOI: 10.2210/pdb2D31/pdb

• Classification: IMMUNE SYSTEM/CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-23 Released: 2006-03-14 
• Deposition Author(s): Shiroishi, M., Kuroki, K., Ose, T., Rasubala, L., Shiratori, I., Arase, H., Tsumoto, K., Kumagai, I., Kohda, D., Maenaka, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.298 
• R-Value Work: 0.235 
• R-Value Observed: 0.239 

Literature

Efficient Leukocyte Ig-like Receptor Signaling and Crystal Structure of Disulfide-linked HLA-G Dimer

Shiroishi, M., Kuroki, K., Ose, T., Rasubala, L., Shiratori, I., Arase, H., Tsumoto, K., Kumagai, I., Kohda, D., Maenaka, K.

(2006) J Biol Chem 281: 10439-10447

• PubMed: 16455647 
• DOI: 10.1074/jbc.M512305200
• Primary Citation of Related Structures:  
  2D31


• PubMed Abstract: 
  

HLA-G is a nonclassical major histocompatibility complex class I (MHCI) molecule, which is expressed in trophoblasts and confers immunological tolerance in the maternal-fetal interface by binding to leukocyte Ig-like receptors (LILRs, also called as LIR/ILT/CD85) and CD8. HLA-G is expressed in disulfide-linked dimer form both in solution and at the cell surface. Interestingly, MHCI dimer formations have been involved in pathogenesis and T cell activation. The structure and receptor binding characteristics of MHCI dimers have never been evaluated. Here we performed binding studies showing that the HLA-G dimer exhibited higher overall affinity to LILRB1/2 than the monomer by significant avidity effects. Furthermore, the cell reporter assay demonstrated that the dimer formation remarkably enhanced the LILRB1-mediated signaling at the cellular level. We further determined the crystal structure of the wild-type dimer of HLA-G with the intermolecular Cys(42)-Cys(42) disulfide bond. This dimer structure showed the oblique configuration to expose two LILR/CD8-binding sites upward from the membrane easily accessible for receptors, providing plausible 1:2 (HLA-G dimer:receptors) complex models. These results indicated that the HLA-G dimer conferred increased avidity in a proper structural orientation to induce efficient LILR signaling, resulting in the dominant immunosuppressive effects. Moreover, structural and functional implications for other MHCI dimers observed in activated T cells and the pathogenic allele, HLA-B27, are discussed.

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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, D	276	Homo sapiens	Mutation(s): 0  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, E	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	C, F	9	Homo sapiens	Mutation(s): 0  Gene Names: H2AX, H2AFX
Find proteins for P16104 (Homo sapiens) Explore P16104  Go to UniProtKB:  P16104
NIH Common Fund Data Resources
PHAROS  P16104 GTEx  ENSG00000188486

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.298 
• R-Value Work: 0.235 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.641	α = 90
b = 127.807	β = 90
c = 72.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-23 
• Released Date: 2006-03-14 
Deposition Author(s): Shiroishi, M., Kuroki, K., Ose, T., Rasubala, L., Shiratori, I., Arase, H., Tsumoto, K., Kumagai, I., Kohda, D., Maenaka, K.

Revision History 

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-02-05
  Changes: Database references, Derived calculations
• Version 1.4: 2020-02-19
  Changes: Data collection, Derived calculations, Source and taxonomy