1HSB

DIFFERENT LENGTH PEPTIDES BIND TO HLA-AW68 SIMILARLY AT THEIR ENDS BUT BULGE OUT IN THE MIDDLE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle.

Guo, H.C.Jardetzky, T.S.Garrett, T.P.Lane, W.S.Strominger, J.L.Wiley, D.C.

(1992) Nature 360: 364-366

  • DOI: 10.1038/360364a0

  • PubMed Abstract: 
  • We report here the determination and refinement to 1.9 A resolution by X-ray cryo-crystallography the structure of HLA-Aw68. The averaged image from the collection of bound, endogenous peptides clearly shows the atomic structure at the first three an ...

    We report here the determination and refinement to 1.9 A resolution by X-ray cryo-crystallography the structure of HLA-Aw68. The averaged image from the collection of bound, endogenous peptides clearly shows the atomic structure at the first three and last two amino acids in the peptides but no connected electron density in between. This suggests that bound peptides, held at both ends, take alternative pathways and could be of different lengths by bulging out in the middle. Peptides eluted from HLA-Aw68 include peptides of 9, 10 and 11 amino acids, a direct indication of the length heterogeneity of tightly bound peptides. Peptide sequencing shows relatively conserved 'anchor' residues at position 2 and the carboxy-terminal residue. Conserved binding sites for the peptide N and C termini at the ends of the class I major histocompatibility complex binding groove are apparently dominant in producing the long half-lives of peptide binding and the peptide-dependent stabilization of the class I molecule's structure.


    Related Citations: 
    • 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
    • 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
    • Atomic Structure of a Human Mhc Molecule Presenting an Influenza Virus Peptide
      Silver, M.L.,Guo, H.-C.,Strominger, J.L.,Wiley, D.C.
      (1992) Nature 360: 367
    • Comparison of a Specificity Pocket in Three Human Histocompatibility Antigens: Hla-Aw68, Hla-A2 and Hla-B27
      Guo, H.-C.,Madden, D.R.,Strominger, J.L.,Wiley, D.C.
      () TO BE PUBLISHED --: --
    • 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 Structure of Hla-B27 Reveals Nonamer Self-Peptides Bound in an Extended Conformation
      Madden, D.R.,Gorga, J.C.,Strominger, J.L.,Wiley, D.C.
      (1991) Nature 353: 321
    • The Three-Dimensional Structure of Hla-B27 at 2.1 Angstroms Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc
      Madden, D.R.,Gorga, J.C.,Strominger, J.L.,Wiley, D.C.
      (1992) Cell 70: 1035
    • Specificity Pockets for the Side Chains of Peptide Antigens in Hla-Aw68
      Garrett, T.P.J.,Saper, M.A.,Bjorkman, P.J.,Strominger, J.L.,Wiley, D.C.
      (1989) Nature 342: 692
    • Different Length Peptides Bind to Hla-Aw68 Similarly at Their Ends But Bulge Out in the Middle
      Guo, H.-C.,Jardetzky, T.S.,Garrett, T.P.J.,Lane, W.S.,Strominger, J.L.,Wiley, D.C.
      (1992) Nature 360: 364
    • 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 Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-AW68.1)
A
270Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P01891 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P01891
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA 2-MICROGLOBULIN
B
99Homo 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
BOUND PEPTIDE FRAGMENT
C
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ALA
Query on ALA

Download SDF File 
Download CCD File 
A
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.430α = 90.00
b = 78.469β = 90.00
c = 111.904γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance