5DEF

Crystal structure of B*27:04 complex bound to the pVIPR peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Increased Conformational Flexibility of HLA-B*27 Subtypes Associated With Ankylosing Spondylitis.

Loll, B.Fabian, H.Huser, H.Hee, C.S.Ziegler, A.Uchanska-Ziegler, B.Ziegler, A.

(2016) Arthritis Rheumatol 68: 1172-1182

  • DOI: 10.1002/art.39567
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dissimilarities in antigen processing and presentation are known to contribute to the differential association of HLA-B*27 subtypes with the inflammatory rheumatic disease ankylosing spondylitis (AS). In support of this notion, previous x-ray crystal ...

    Dissimilarities in antigen processing and presentation are known to contribute to the differential association of HLA-B*27 subtypes with the inflammatory rheumatic disease ankylosing spondylitis (AS). In support of this notion, previous x-ray crystallographic data showed that peptides can be displayed by almost identical HLA-B*27 molecules in a subtype-dependent manner, allowing cytotoxic T lymphocytes to distinguish between these subtypes. For example, a human self-peptide derived from vasoactive intestinal peptide receptor type 1 (pVIPR; sequence RRKWRRWHL) is displayed in a single conformation by B*27:09 (which is not associated with AS), while B*27:05 (which is associated with AS) presents the peptide in a dual binding mode. In addition, differences in conformational flexibility between these subtypes might affect their stability or antigen presentation capability. This study was undertaken to investigate B*27:04 and B*27:06, another pair of minimally distinct HLA-B*27 subtypes, to assess whether dual peptide conformations or structural dynamics play a role in the initiation of AS.


    Organizational Affiliation

    Ziegler Biosolutions, Waldshut-Tiengen, Germany.,Universität Bonn, Bonn, Germany.,Freie Universität Berlin, Berlin, Germany.,Charité-Universitätsmedizin Berlin and Freie Universität Berlin, Berlin, Germany.,Universität Basel, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-27 alpha chain
A
276Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P01889 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P01889
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
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 derived from VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1 (pVIPR)
C
9Homo sapiensMutation(s): 0 
Gene Names: VIPR1
Find proteins for P32241 (Homo sapiens)
Go to Gene View: VIPR1
Go to UniProtKB:  P32241
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.770α = 90.00
b = 82.160β = 90.00
c = 109.863γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanySFB 449
DFGGermanyUC 8/1-3

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2016-01-20
    Type: Database references
  • Version 1.2: 2016-01-27
    Type: Database references