3BZE

The human non-classical major histocompatibility complex molecule HLA-E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Subtle changes in peptide conformation profoundly affect recognition of the non-classical MHC class I molecule HLA-E by the CD94-NKG2 natural killer cell receptors

Hoare, H.L.Sullivan, L.C.Clements, C.S.Ely, L.K.Beddoe, T.Henderson, K.N.Lin, J.Reid, H.H.Brooks, A.G.Rossjohn, J.

(2008) J Mol Biol 377: 1297-1303

  • DOI: https://doi.org/10.1016/j.jmb.2008.01.098
  • Primary Citation of Related Structures:  
    3BZE, 3BZF

  • PubMed Abstract: 

    Human leukocyte antigen (HLA)-E is a non-classical major histocompatibility complex class I molecule that binds peptides derived from the leader sequences of other HLA class I molecules. Natural killer cell recognition of these HLA-E molecules, via the CD94-NKG2 natural killer family, represents a central innate mechanism for monitoring major histocompatibility complex expression levels within a cell. The leader sequence-derived peptides bound to HLA-E exhibit very limited polymorphism, yet subtle differences affect the recognition of HLA-E by the CD94-NKG2 receptors. To better understand the basis for this peptide-specific recognition, we determined the structure of HLA-E in complex with two leader peptides, namely, HLA-Cw*07 (VMAPRALLL), which is poorly recognised by CD94-NKG2 receptors, and HLA-G*01 (VMAPRTLFL), a high-affinity ligand of CD94-NKG2 receptors. A comparison of these structures, both of which were determined to 2.5-A resolution, revealed that allotypic variations in the bound leader sequences do not result in conformational changes in the HLA-E heavy chain, although subtle changes in the conformation of the peptide within the binding groove of HLA-E were evident. Accordingly, our data indicate that the CD94-NKG2 receptors interact with HLA-E in a manner that maximises the ability of the receptors to discriminate between subtle changes in both the sequence and conformation of peptides bound to HLA-E.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, alpha chain E
A, C, E, G
273Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P13747 (Homo sapiens)
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Go to UniProtKB:  P13747
PHAROS:  P13747
GTEx:  ENSG00000204592 
Entity Groups  
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UniProt GroupP13747
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, D, F, H
100Homo sapiensMutation(s): 0 
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Find proteins for P61769 (Homo sapiens)
Explore P61769 
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
leader peptide of HLA class I histocompatibility antigen, alpha chain GI [auth P],
J [auth Q],
K [auth R],
L [auth S]
9N/AMutation(s): 0 
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Find proteins for P17693 (Homo sapiens)
Explore P17693 
Go to UniProtKB:  P17693
PHAROS:  P17693
GTEx:  ENSG00000204632 
Entity Groups  
UniProt GroupP17693
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.778α = 90
b = 73.354β = 112.7
c = 131.535γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description