8UMO | pdb_00008umo

Murine CD94-NKG2A receptor in complex with Qa-1b presenting AMAPRTLLL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.251 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure of the murine CD94-NKG2A receptor in complex with Qa-1 b presenting an MHC-I leader peptide.

MacLachlan, B.J.Sullivan, L.C.Brooks, A.G.Rossjohn, J.Vivian, J.P.

(2024) FEBS J 291: 1530-1544

  • DOI: https://doi.org/10.1111/febs.17050
  • Primary Citation Related Structures: 
    8UMO

  • PubMed Abstract: 

    The heterodimeric natural killer cells antigen CD94 (CD94)-NKG2-A/NKG2-B type II integral membrane protein (NKG2A) receptor family expressed on human and mouse natural killer (NK) cells monitors global major histocompatibility complex (MHC) class I cell surface expression levels through binding to MHC class Ia-derived leader sequence peptides presented by HLA class I histocompatibility antigen, alpha chain E (HLA-E; in humans) or H-2 class I histocompatibility antigen, D-37 (Qa-1 b ; in mice). Although the molecular basis underpinning human CD94-NKG2A recognition of HLA-E is known, the equivalent interaction in the murine setting is not. By determining the high-resolution crystal structure of murine CD94-NKG2A in complex with Qa-1 b presenting the Qa-1 determinant modifier peptide (QDM), we resolved the mode of binding. Compared to the human homologue, the murine CD94-NKG2A-Qa-1 b -QDM displayed alterations in the distribution of interactions across CD94 and NKG2A subunits that coincide with differences in electrostatic complementarity of the ternary complex and the lack of cross-species reactivity. Nevertheless, we show that Qa-1b could be modified through W65R + N73I mutations to mimic HLA-E, facilitating binding with both human and murine CD94-NKG2A. These data underscore human and murine CD94-NKG2A cross-species heterogeneity and provide a foundation for humanising Qa-1b in immune system models.


  • Organizational Affiliation
    • Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.

Macromolecule Content 

  • Total Structure Weight: 72.86 kDa 
  • Atom Count: 5,140 
  • Modeled Residue Count: 614 
  • Deposited Residue Count: 623 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-37 alpha chain278Mus musculusMutation(s): 0 
Gene Names: H2-T23
UniProt
Find proteins for P06339 (Mus musculus)
Explore P06339 
Go to UniProtKB:  P06339
Entity Groups
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UniProt GroupP06339
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 1 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Killer cell lectin-like receptor, subfamily D, member 1C [auth J]120Mus musculusMutation(s): 0 
Gene Names: Klrd1
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Killer cell lectin-like receptor subfamily C, member 1D [auth K]117Mus musculusMutation(s): 0 
Gene Names: Klrc1
UniProt
Find proteins for Q9WU32 (Mus musculus)
Explore Q9WU32 
Go to UniProtKB:  Q9WU32
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UniProt GroupQ9WU32
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Qdm peptideE [auth P]9Mus musculusMutation(s): 0 
UniProt
Find proteins for P01897 (Mus musculus)
Explore P01897 
Go to UniProtKB:  P01897
Entity Groups
UniProt GroupP01897
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.251 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.17α = 90
b = 65.091β = 90
c = 198.574γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedAustralia--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Structure summary
  • Version 1.2: 2024-04-17
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Structure summary