1MHE | pdb_00001mhe

THE HUMAN NON-CLASSICAL MAJOR HISTOCOMPATIBILITY COMPLEX MOLECULE HLA-E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.235 (Depositor) 
  • R-Value Work: 
    0.202 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural features impose tight peptide binding specificity in the nonclassical MHC molecule HLA-E.

O'Callaghan, C.A.Tormo, J.Willcox, B.E.Braud, V.M.Jakobsen, B.K.Stuart, D.I.McMichael, A.J.Bell, J.I.Jones, E.Y.

(1998) Mol Cell 1: 531-541

  • DOI: https://doi.org/10.1016/s1097-2765(00)80053-2
  • Primary Citation Related Structures: 
    1MHE

  • PubMed Abstract: 

    The crystal structure of the nonclassical human class lb MHC molecule HLA-E has been determined in complex with a prototypic ligand, the nonamer peptide (VMAPRTVLL), derived from the highly conserved residues 3-11 of the human MHC class la leader sequence. The mode of peptide binding retains some of the standard features observed in MHC class la complexes, but novel features imply that HLA-E has evolved to mediate specific binding to a tightly defined set of almost identical hydrophobic peptides from the highly conserved class l leader sequences. These molecular adaptations make HLA-E a rigorous checkpoint at the cell surface reporting on the integrity of the antigen processing pathway to CD94/NKG2 receptor-bearing natural killer cells.


  • Organizational Affiliation
    • Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 89.25 kDa 
  • Atom Count: 6,293 
  • Modeled Residue Count: 764 
  • Deposited Residue Count: 766 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN HLA-E
A, C
274Homo sapiensMutation(s): 0 
Gene Names: HLA-E
UniProt & NIH Common Fund Data Resources
Find proteins for P13747 (Homo sapiens)
Explore P13747 
Go to UniProtKB:  P13747
PHAROS:  P13747
GTEx:  ENSG00000204592 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13747
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-2-MICROGLOBULIN
B, D
100Homo sapiensMutation(s): 0 
Gene Names: BETA-2-MICROGLOBULIN
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PEPTIDE (VMAPRTVLL)E [auth P],
F [auth Q]
9N/AMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.235 (Depositor) 
  • R-Value Work:  0.202 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.2α = 90
b = 182.2β = 90
c = 88.4γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-23
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Data collection, Structure summary