5IB5

Crystal structure of HLA-B*27:09 complexed with the self-peptide pVIPR and Copper


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Metal-triggered conformational reorientation of a self-peptide bound to a disease-associated HLA-B*27 subtype.

Driller, R.Ballaschk, M.Schmieder, P.Uchanska-Ziegler, B.Ziegler, A.Loll, B.

(2019) J Biol Chem 

  • DOI: https://doi.org/10.1074/jbc.RA119.008937
  • Primary Citation of Related Structures:  
    5IB1, 5IB2, 5IB3, 5IB4, 5IB5

  • PubMed Abstract: 
  • Conformational changes of major histocompatibility complex (MHC) antigens have the potential to be recognized by T cells and may arise from polymorphic variation of the MHC molecule, the binding of modifying ligands, or both. Here, we investigated whether metal ions could affect allele-dependent structural variation of the two minimally distinct human leukocyte antigen (HLA)-B*27:05 and HLA-B*27:09 subtypes, which exhibit differential association with the rheumatic disease ankylosing spondylitis (AS) ...

    Conformational changes of major histocompatibility complex (MHC) antigens have the potential to be recognized by T cells and may arise from polymorphic variation of the MHC molecule, the binding of modifying ligands, or both. Here, we investigated whether metal ions could affect allele-dependent structural variation of the two minimally distinct human leukocyte antigen (HLA)-B*27:05 and HLA-B*27:09 subtypes, which exhibit differential association with the rheumatic disease ankylosing spondylitis (AS). We employed NMR spectroscopy and X-ray crystallography coupled with ensemble refinement to study the AS-associated HLA-B*27:05 subtype and the AS-nonassociated HLA-B* 27:09 in complex with the self-peptide pVIPR (RRKWRRWHL). Both techniques revealed that pVIPR exhibits a higher degree of flexibility when complexed with HLA-B*27:05 than with HLA-B*27:09. Furthermore, we found that the binding of the metal ion Cu 2+ or Ni 2+ , but not Mn 2+ , Zn 2+ , or Hg 2+ , affects the structure of a pVIPR-bound HLA-B*27 molecule in a subtype-dependent manner. In HLA-B*27:05, the metals triggered conformational reorientations of pVIPR, but no such structural changes were observed in the HLA-B*27:09 subtype, with or without bound metal ion. These observations provide the first demonstration that not only major histocompatibility complex class II, but also class I, molecules can undergo metal ion-induced conformational alterations. Our findings suggest that metals may have a role in triggering rheumatic diseases such as AS and also have implications for the molecular basis of metal-induced hypersensitivities and allergies.


    Organizational Affiliation

    Institut für Chemie/Biochemie, AG Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany; MoloX GmbH, Takustrasse 6, 14195 Berlin, Germany. Electronic address: loll@chemie.fu-berlin.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-27 alpha chain
A, D
276Homo sapiensMutation(s): 1 
Gene Names: HLA-BHLAB
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Find proteins for P01889 (Homo sapiens)
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PHAROS:  P01889
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UniProt GroupP01889
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
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UniProt GroupP61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vasoactive intestinal polypeptide receptor 1
C, F
9Homo sapiensMutation(s): 0 
Gene Names: VIPR1
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Find proteins for P32241 (Homo sapiens)
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Go to UniProtKB:  P32241
PHAROS:  P32241
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UniProt GroupP32241
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.004α = 90
b = 81.677β = 96.74
c = 126.474γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Data collection, Database references