4PGC

MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGN(3,5-diiodotyrosine)PAL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The first step of peptide selection in antigen presentation by MHC class I molecules.

Garstka, M.A.Fish, A.Celie, P.H.Joosten, R.P.Janssen, G.M.Berlin, I.Hoppes, R.Stadnik, M.Janssen, L.Ovaa, H.van Veelen, P.A.Perrakis, A.Neefjes, J.

(2015) Proc Natl Acad Sci U S A 112: 1505-1510

  • DOI: 10.1073/pnas.1416543112
  • Primary Citation of Related Structures:  
    4PGC, 4PGD, 4PGE, 4PGB, 4PG9

  • PubMed Abstract: 
  • MHC class I molecules present a variable but limited repertoire of antigenic peptides for T-cell recognition. Understanding how peptide selection is achieved requires mechanistic insights into the interactions between the MHC I and candidate peptides ...

    MHC class I molecules present a variable but limited repertoire of antigenic peptides for T-cell recognition. Understanding how peptide selection is achieved requires mechanistic insights into the interactions between the MHC I and candidate peptides. We find that, at first encounter, MHC I H-2K(b) considers a wide range of peptides, including those with expanded N termini and unfitting anchor residues. Discrimination occurs in the second step, when noncanonical peptides dissociate with faster exchange rates. This second step exhibits remarkable temperature sensitivity, as illustrated by numerous noncanonical peptides presented by H-2K(b) in cells cultured at 26 °C relative to 37 °C. Crystallographic analyses of H-2K(b)-peptide complexes suggest that a conformational adaptation of H-2K(b) drives the decisive step in peptide selection. We propose that MHC class I molecules consider initially a large peptide pool, subsequently refined by a temperature-sensitive induced-fit mechanism to retain the canonical peptide repertoire.


    Organizational Affiliation

    Departments of Cell Biology and j.neefjes@nki.nl.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-B alpha chainAD304Mus musculusMutation(s): 0 
Gene Names: H2-K1H2-K
Find proteins for P01901 (Mus musculus)
Explore P01901 
Go to UniProtKB:  P01901
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBE100Mus musculusMutation(s): 1 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sendai virus nucleoproteinCF9Murine respirovirusMutation(s): 0 
Find proteins for O57286 (Sendai virus (strain Ohita))
Explore O57286 
Go to UniProtKB:  O57286
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown helical fragmentH13Escherichia coli BL21(DE3)Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B, D, E
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYI
Query on TYI
C,FL-PEPTIDE LINKINGC9 H9 I2 N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.179α = 90
b = 90.303β = 111.58
c = 89.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands--

Revision History 

  • Version 1.0: 2015-01-07
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Database references
  • Version 1.3: 2015-02-11
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence