1LK2

1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A peptide that antagonizes TCR-mediated reactions with both syngeneic and allogeneic agonists: functional and structural aspects.

Rudolph, M.G.Shen, L.Q.Lamontagne, S.A.Luz, J.G.Delaney, J.R.Ge, Q.Cho, B.K.Palliser, D.McKinley, C.A.Chen, J.Wilson, I.A.Eisen, H.N.

(2004) J Immunol 172: 2994-3002

  • DOI: https://doi.org/10.4049/jimmunol.172.5.2994
  • Primary Citation of Related Structures:  
    1LK2

  • PubMed Abstract: 

    We identify and consider some characteristics of a peptide antagonist for the Ag-specific receptor on 2C cells (the 2C TCR). The peptide, GNYSFYAL (called GNY), binds to H-2K(b), and a very high-resolution crystal structure of the GNY-K(b) complex at 1.35 A is described. Although the GNY peptide does not bind to L(d), the potency of GNY-K(b) as an antagonist is evident from its ability to specifically inhibit 2C TCR-mediated reactions to an allogenic agonist complex (QLSPFPFDL-L(d)), as well as to a syngeneic agonist complex (SIYRYYGL-K(b)). The crystal structure and the activities of alanine-substituted peptide variants point to the properties of the peptide P4 side chain and the conformation of the Tyr-P6 side chain as the structural determinants of GNYSFYAL antagonist activity.


  • Organizational Affiliation

    Center for Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Markus.Rudolph@bio.uni-goettingen.de


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN274Mus musculusMutation(s): 0 
UniProt
Find proteins for P01901 (Mus musculus)
Explore P01901 
Go to UniProtKB:  P01901
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UniProt GroupP01901
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 0 
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
INSULIN RECEPTOR, BETA-SUBUNITC [auth P]8N/AMutation(s): 0 
UniProt
Find proteins for P15208 (Mus musculus)
Explore P15208 
Go to UniProtKB:  P15208
Entity Groups  
UniProt GroupP15208
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.549α = 90
b = 87.65β = 90
c = 45.118γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary