4JO8 | pdb_00004jo8

Crystal structure of the activating Ly49H receptor in complex with m157 (G1F strain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.259 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.304 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Targeting of a natural killer cell receptor family by a viral immunoevasin

Berry, R.Ng, N.Saunders, P.M.Vivian, J.P.Lin, J.Deuss, F.A.Corbett, A.J.Forbes, C.A.Widjaja, J.M.Sullivan, L.C.McAlister, A.D.Perugini, M.A.Call, M.J.Scalzo, A.A.Degli-Esposti, M.A.Coudert, J.D.Beddoe, T.Brooks, A.G.Rossjohn, J.

(2013) Nat Immunol 14: 699-705

  • DOI: https://doi.org/10.1038/ni.2605
  • Primary Citation Related Structures: 
    4JO8

  • PubMed Abstract: 

    Activating and inhibitory receptors on natural killer (NK) cells have a crucial role in innate immunity, although the basis of the engagement of activating NK cell receptors is unclear. The activating receptor Ly49H confers resistance to infection with murine cytomegalovirus by binding to the 'immunoevasin' m157. We found that m157 bound to the helical stalk of Ly49H, whereby two m157 monomers engaged the Ly49H dimer. The helical stalks of Ly49H lay centrally across the m157 platform, whereas its lectin domain was not required for recognition. Instead, m157 targeted an 'aromatic peg motif' present in stalks of both activating and inhibitory receptors of the Ly49 family, and substitution of this motif abrogated binding. Furthermore, ligation of m157 to Ly49H or Ly49C resulted in intracellular signaling. Accordingly, m157 has evolved to 'tackle the legs' of a family of NK cell receptors.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Australia.

Macromolecule Content 

  • Total Structure Weight: 49.3 kDa 
  • Atom Count: 2,077 
  • Modeled Residue Count: 259 
  • Deposited Residue Count: 426 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
M157269Murid betaherpesvirus 1Mutation(s): 2 
Gene Names: m157
UniProt
Find proteins for Q6XK91 (Murid herpesvirus 1)
Explore Q6XK91 
Go to UniProtKB:  Q6XK91
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XK91
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Killer cell lectin-like receptor 8157Mus musculusMutation(s): 3 
Gene Names: Klra8Ly-49hLy49-hLy49H
UniProt
Find proteins for Q60682 (Mus musculus)
Explore Q60682 
Go to UniProtKB:  Q60682
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60682
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.259 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.304 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.87α = 90
b = 87.87β = 90
c = 133.37γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references, Structure summary
  • Version 1.2: 2013-07-10
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-30
    Changes: Structure summary