Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 94.90 kDa 
• Atom Count: 6777 
• Residue Count: 816 
• Unique protein chains: 5

2ESV

Structure of the HLA-E-VMAPRTLIL/KK50.4 TCR complex

• DOI: 10.2210/pdb2ESV/pdb

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


• Deposited: 2005-10-27 Released: 2006-03-21 
• Deposition Author(s): Hoare, H.L., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.292 
• R-Value Work: 0.214 
• R-Value Observed: 0.218 

Literature

Structural basis for a major histocompatibility complex class Ib-restricted T cell response

Hoare, H.L., Sullivan, L.C., Pietra, G., Clements, C.S., Lee, E.J., Ely, L.K., Beddoe, T., Falco, M., Kjer-Nielsen, L., Reid, H.H., McCluskey, J., Moretta, L., Rossjohn, J., Brooks, A.G.

(2006) Nat Immunol 7: 256-264

• PubMed: 16474394 
• DOI: 10.1038/ni1312
• Primary Citation of Related Structures:  
  2ESV


• PubMed Abstract: 
  

In contrast to antigen-specific immunity orchestrated by major histocompatibility complex (MHC) class Ia molecules, the ancestrally related nonclassical MHC class Ib molecules generally mediate innate immune responses. Here we have demonstrated the structural basis by which the MHC class Ib molecule HLA-E mediates an adaptive MHC-restricted cytotoxic T lymphocyte response to human cytomegalovirus. Highly constrained by host genetics, the response showed notable fine specificity for position 8 of the viral peptide, which is the sole discriminator of self versus nonself. Despite the evolutionary divergence of MHC class Ia and class Ib molecules, the structure of the T cell receptor-MHC class Ib complex was very similar to that of conventional T cell receptor-MHC class Ia complexes. These results emphasize the evolutionary 'ambiguity' of HLA-E, which not only interacts with innate immune receptors but also has the functional capacity to mediate virus-specific cytotoxic T lymphocyte responses during adaptive immunity.

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Organizational Affiliation: 

The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, alpha chain E	A	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-E, HLA-6.2, HLAE
Find proteins for P13747 (Homo sapiens) Explore P13747  Go to UniProtKB:  P13747
NIH Common Fund Data Resources
PHAROS  P13747 GTEx  ENSG00000204592

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
VMAPRTLIL peptide from CMV gpUL40	P	9	N/A	Mutation(s): 0
Find proteins for P16780 (Human cytomegalovirus (strain AD169)) Explore P16780  Go to UniProtKB:  P16780

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
KK50.4 T cell receptor alpha chain	D	199	Homo sapiens	Mutation(s): 0  Gene Names: TRAC, TCRA
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
NIH Common Fund Data Resources
PHAROS  P01848

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
KK50.4 T cell receptor beta chain	E	240	Homo sapiens	Mutation(s): 0  Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens) Explore P01850  Go to UniProtKB:  P01850

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	B, D, E	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.292 
• R-Value Work: 0.214 
• R-Value Observed: 0.218 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 235.096	α = 90
b = 41.462	β = 114.66
c = 112.471	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-27 
• Released Date: 2006-03-21 
Deposition Author(s): Hoare, H.L., Rossjohn, J.

Revision History 

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance