Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.31 kDa 
• Atom Count: 3309 
• Residue Count: 374 
• Unique protein chains: 3

4AEN

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

• DOI: 10.2210/pdb4AEN/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-11 Released: 2012-08-01 
• Deposition Author(s): Schlundt, A., Guenther, S., Sticht, J., Wieczorek, M., Roske, Y., Heinemann, U., Freund, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

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

• PubMed: 22820093 
• DOI: 10.1016/j.jmb.2012.07.008
• Primary Citation of Related Structures:  
  4AEN, 4AH2


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN	A	207	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN	B	199	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN	C	16	Homo sapiens	Mutation(s): 0  Gene Names: CD74, DHLAG
Find proteins for P04233 (Homo sapiens) Explore P04233  Go to UniProtKB:  P04233
NIH Common Fund Data Resources
PHAROS:  P04233 GTEx:  ENSG00000019582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.196	α = 90
b = 145.111	β = 90
c = 108.777	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-11 
• Released Date: 2012-08-01 
Deposition Author(s): Schlundt, A., Guenther, S., Sticht, J., Wieczorek, M., Roske, Y., Heinemann, U., Freund, C.

Revision History 

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Database references