Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89860.29 
• Atom Count: 6124 
• Residue Count: 770 
• 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)


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.2 Å
• R-Value Free: 0.298 
• R-Value Work: 0.235 

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


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: HLA-G Go to UniProtKB:  P17693

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B, E	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
9-mer peptide from Histone H2A	C, F	9	Homo sapiens	Mutation(s): 0  Gene Names: H2AFX (H2AX)
Find proteins for P16104 (Homo sapiens) Go to Gene View: H2AFX Go to UniProtKB:  P16104

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.2 Å
• R-Value Free: 0.298 
• R-Value Work: 0.235 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 94.641	α = 90.00
b = 127.807	β = 90.00
c = 72.580	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance