2CLR

THREE DIMENSIONAL STRUCTURE OF A PEPTIDE EXTENDING OUT ONE END OF A CLASS I MHC BINDING SITE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Three-dimensional structure of a peptide extending from one end of a class I MHC binding site.

Collins, E.J., Garboczi, D.N., Wiley, D.C.

(1994) Nature 371: 626-629

  • DOI: 10.1038/371626a0

  • PubMed Abstract: 

    • Class I major histocompatibility complex (MHC) molecules present peptides to CD8+ T cells for immunological surveillance (reviewed in ref. 1). The structures of complexes of class I MHC molecules with octamer, nonamer and decamer peptides determined ...

    Class I major histocompatibility complex (MHC) molecules present peptides to CD8+ T cells for immunological surveillance (reviewed in ref. 1). The structures of complexes of class I MHC molecules with octamer, nonamer and decamer peptides determined until now show a common binding mode, with both peptide termini bound in conserved pockets at the ends of the peptide binding site. Length variations were accommodated by the peptide bulging or zig-zagging in the middle. Here we describe the structure of a decamer peptide which binds with the carboxy-terminal residue positioned outside the peptide binding site. Several protein side chains have rearranged to allow the peptide to exit. The structure suggests that even longer peptides could bind. The energetic effect of the altered mode of binding has been assessed by measuring the stability of the complex to thermal denaturation. Peptides bound in this novel manner are stable at physiological temperature, raising questions about their role in T-cell recognition and their production by proteolytic processing.

    Related Citations: 
    • Comparison of the P2 Specificity Pocket in Three Human Histocompatibility Antigens: Hla-A(Asterisk)6801, Hla-A(Asterisk)0201, and Hla-B(Asterisk)2705
      Guo, H.-C.,Madden, D.R.,Silver, M.L.,Jardetzky, T.S.,Gorga, J.C.,Strominger, J.L.,Wiley, D.C.
      (1993) Proc.Natl.Acad.Sci.USA 90: 8053
    • Hla-A2-Peptide Complexes: Refolding and Crystallization of Molecules Expressed in Escherichia Coli and Complexed with Single Antigenic Peptides
      Garboczi, D.N.,Hung, D.T.,Wiley, D.C.
      (1992) Proc.Natl.Acad.Sci.USA 89: 3429
    • Five Viral Peptide-Hla-A2 Co-Crystals: Simultaneous Space Group Determination and X-Ray Data Collection
      Garboczi, D.N.,Madden, D.R.,Wiley, D.C.
      (1994) J.Mol.Biol. 239: 581
    • The Antigenic Identity of Peptide-Mhc Complexes a Comparison of the Conformations of Five Viral Peptides Presented by Hla-A2
      Madden, D.R.,Garboczi, D.N.,Wiley, D.C.
      (1993) Cell 75: 693
    • Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution
      Saper, M.A.,Bjorkman, P.J.,Wiley, D.C.
      (1991) J.Mol.Biol. 219: 277
    • The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens
      Bjorkman, P.J.,Saper, M.A.,Samraoui, B.,Bennett, W.S.,Strominger, J.L.,Wiley, D.C.
      (1987) Nature 329: 512
    • Structure of the Human Class I Histocompatibility Antigen, Hla-A2
      Bjorkman, P.J.,Saper, M.A.,Samraoui, B.,Bennett, W.S.,Strominger, J.L.,Wiley, D.C.
      (1987) Nature 329: 506
    • Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes
      Bjorkman, P.J.,Strominger, J.L.,Wiley, D.C.
      (1985) J.Mol.Biol. 186: 205

    Organizational Affiliation: 

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) (ALPHA CHAIN)
A, D
275Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P04439 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P04439
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA 2-MICROGLOBULIN
B, E
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DECAMERIC PEPTIDE FROM CALRETICULIN
C, F
10Homo sapiensMutation(s): 0 
Gene Names: CALR (CRTC)
Find proteins for P27797 (Homo sapiens)
Go to Gene View: CALR
Go to UniProtKB:  P27797
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.236 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.410α = 81.99
b = 62.909β = 76.43
c = 74.810γ = 78.06
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-03-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance