1A9B

DECAMER-LIKE CONFORMATION OF A NANO-PEPTIDE BOUND TO HLA-B3501 DUE TO NONSTANDARD POSITIONING OF THE C-TERMINUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus.

Menssen, R.Orth, P.Ziegler, A.Saenger, W.

(1999) J.Mol.Biol. 285: 645-653

  • DOI: 10.1006/jmbi.1998.2363
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The N and C termini of peptides presented by major histocompatibility complex (MHC) class I molecules are held within the peptide binding groove by a network of hydrogen bonds to conserved MHC residues. However, the published structure of the human a ...

    The N and C termini of peptides presented by major histocompatibility complex (MHC) class I molecules are held within the peptide binding groove by a network of hydrogen bonds to conserved MHC residues. However, the published structure of the human allele HLA-B*3501 complexed with the nef octa-peptide VPLRPMTY, revealed non-standard positioning for both peptide termini. To investigate whether these deviations are indeed related to the length of the nef-peptide, we have determined the structure of HLA-B*3501 presenting a nona-peptide to 2.5 A resolution. A comparison of HLA-B*3501/peptide complexes with structures of other HLA molecules exhibits allele-specific properties of HLA-B*3501, as well as peptide-induced structural changes. Independent of the length of the bound peptide, HLA-B*3501 positions the peptide C terminus significantly closer to the alpha1-helix and nearer to the A pocket than observed for other HLA class I/peptide complexes. This reorientation is accompanied by a shift within the N-terminal part of the alpha2-helix towards the middle of the binding groove. Due to the short distance between the N and C termini, the nona-peptide is compressed and forced to zig-zag vertically within the binding groove. Its conformation rather resembles that of a deca-peptide than of other nona-peptides bound to class I molecules. Superposition of both HLA-B*3501/peptide complexes additionally reveals a significant, peptide-dependent deviation between the N-terminal parts of the alpha1-helices which might be due to different positioning of the peptide N termini. Taken together, these data illustrate the strong interdependence between the HLA class I molecule and the bound peptide.


    Organizational Affiliation

    Institut für Immungenetik Universitätsklinikum Charité, Humboldt-Universität zu Berlin, Spandauer Damm 130, Berlin, D-14050, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B*3501 (ALPHA CHAIN)
A, D
277Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P30685 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30685
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
PEPTIDE LPPLDITPY
C, F
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.740α = 90.00
b = 116.390β = 90.00
c = 169.340γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance