1W72

Crystal structure of HLA-A1:MAGE-A1 in complex with Fab-Hyb3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 

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This is version 1.1 of the entry. See complete history. 


Literature

A Major Histocompatibility Complex.Peptide- Restricted Antibody and T Cell Receptor Molecules Recognize Their Target by Distinct Binding Modes: Crystal Structure of Human Leukocyte Antigen (Hla)-A1.Mage-A1 in Complex with Fab-Hyb3

Hulsmeyer, M., Chames, P., Hillig, R.C., Stanfield, R.L., Held, G., Coulie, P.G., Alings, C., Wille, G., Saenger, W., Uchanska-Ziegler, B., Hoogenboom, H.R., Ziegler, A.

(2005) J Biol Chem 280: 2972

  • DOI: 10.1074/jbc.M411323200
  • Primary Citation of Related Structures:  
    1W72

  • PubMed Abstract: 

    • Antibodies with T cell receptor-like specificity possess a considerable diagnostic and therapeutic potential, but the structural basis of the interaction between an antibody and an histocompatibility antigen has so far not been determined. We present ...

    Antibodies with T cell receptor-like specificity possess a considerable diagnostic and therapeutic potential, but the structural basis of the interaction between an antibody and an histocompatibility antigen has so far not been determined. We present here the crystal structure (at 2.15 A resolution) of the recombinant, affinity-matured human antibody fragment Fab-Hyb3 bound to the tumor-associated human leukocyte antigen (HLA)/peptide complex HLA-A1.MAGE-A1. Fab-Hyb3 employs a diagonal docking mode resembling that of T cell receptors. However, other than these natural ligands, the antibody uses only four of its six complementarity-determining regions for direct interactions with the target. It recognizes the C-terminal half of the MAGE-A1 peptide, the HLA-A1 alpha1-helix, and N-terminal residues of the alpha2-helix, accompanied by a large tilting angle between the two types of molecules within the complex. Interestingly, only a single hydrogen bond between a peptide side chain and Fab-Hyb3 contributes to the interaction, but large buried surface areas with pronounced shape complementarity assure high affinity and specificity for MAGE-A1. The HLA-A1.MAGE-A1.antibody structure is discussed in comparison with those of natural ligands recognizing HLA.peptide complexes.

    Related Citations: 
    • Direct Selection of a Human Antibody Fragment Directed Against the Tumor T-Cell Epitope Hla-A1- Mage-A1 from a Nonimmunized Phage-Fab Library
      Chames, P., Hufton, S.E., Coulie, P.G., Uchanska-Ziegler, B., Hoogenboom, H.R.
      (2000) Proc Natl Acad Sci U S A 97: 7969
    • Tcr-Like Human Antibodies Expressed on Human Ctls Mediate Antibody Affinity-Dependent Cytolytic Activity
      Chames, P., Willemsen, R.A., Rojas, G., Dieckmann, D., Rem, L., Schuler, G., Bolhuis, R.L., Hoogenboom, H.R.
      (2002) J Immunol 169: 1110
    Organizational Affiliation: 

    Institut für Chemie/Kristallographie, Freie Universität Berlin, 14195 Berlin, Germany, Cellectis, 93235 Romainville, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA CLASS I HISTOCOMPATIBILITY ANTIGENA, D274Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
GTEx  ENSG00000206503
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-2-MICROGLOBULINB, E100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
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PHAROS  P61769
GTEx  ENSG00000166710
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MELANOMA-ASSOCIATED ANTIGEN 1C, F9Homo sapiensMutation(s): 0 
Gene Names: MAGEA1, MAGE1, MAGE1A
Find proteins for P43355 (Homo sapiens)
Explore P43355 
Go to UniProtKB:  P43355
NIH Common Fund Data Resources
PHAROS  P43355
GTEx  ENSG00000198681
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HYB3 HEAVY CHAINH, I223Homo sapiensMutation(s): 0 
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
HYB3 LIGHT CHAINL, M210Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download CCD File 
A, I, M
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.359α = 90
b = 50.05β = 109.85
c = 136.705γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance