4AH2

HLA-DR1 with covalently linked CLIP106-120 in canonical orientation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Peptide Linkage to the Alpha-Subunit of Mhcii Creates a Stably Inverted Antigen Presentation Complex.

Schlundt, A.Gunther, S.Sticht, J.Wieczorek, M.Roske, Y.Heinemann, U.Freund, C.

(2012) J Mol Biol 423: 294

  • DOI: 10.1016/j.jmb.2012.07.008
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Class II proteins of the major histocompatibility complex (MHCII) typically present exogenous antigenic peptides to cognate T cell receptors of CD4-T lymphocytes. The exact conformation of peptide-MHCII complexes (pMHCII) can vary depending on the le ...

    Class II proteins of the major histocompatibility complex (MHCII) typically present exogenous antigenic peptides to cognate T cell receptors of CD4-T lymphocytes. The exact conformation of peptide-MHCII complexes (pMHCII) can vary depending on the length, register and orientation of the bound peptide. We have recently found the self-peptide CLIP (class-II-associated invariant chain-derived peptide) to adopt a dynamic bidirectional binding mode with regard to the human MHCII HLA-DR1 (HLA, human leukocyte antigen). We suggested that inversely bound peptides could activate specific T cell clones in the context of autoimmunity. As a first step to prove this hypothesis, pMHC complexes restricted to either the canonical or the inverted peptide orientation have to be constructed. Here, we show that genetically encoded linkage of CLIP and two other antigenic peptides to the HLA-DR1 α-chain results in stable complexes with inversely bound ligands. Two-dimensional NMR and biophysical analyses indicate that the CLIP-bound pMHC(inv) complex (pMHC(inv), inverted MHCII-peptide complex) displays high thermodynamic stability but still allows for the exchange against higher-affinity viral antigen. Complemented by comparable data on a corresponding β-chain-fused canonical HLA-DR1/CLIP complex, we further show that linkage of CLIP leads to a binding mode exactly the same as that of the corresponding unlinked constructs. We suggest that our approach constitutes a general strategy to create pMHC(inv) complexes. Such engineering is needed to create orientation-specific antibodies and raise T cells to study phenomena of autoimmunity caused by isomeric pMHCs.


    Organizational Affiliation

    Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
A
193Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
Find proteins for P01903 (Homo sapiens)
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN, HLA CLASS II HISTOCOMPATIBILITY ANTIGEN\,DRB1-1 BETA CHAIN
B
229Homo sapiensMutation(s): 0 
Gene Names: CD74
Find proteins for P01911 (Homo sapiens)
Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS  P01911
Find proteins for P04233 (Homo sapiens)
Go to UniProtKB:  P04233
NIH Common Fund Data Resources
PHAROS  P04233
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.644α = 90
b = 65.616β = 90
c = 131.331γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 1.2: 2017-03-15
    Changes: Source and taxonomy