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 

wwPDB Validation 3D Report Full Report


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
  • Also Cited By: 3BO8

  • 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: 
    • 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
    • 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.USA 97: 7969

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
A, D
274Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P04439 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P04439
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2-MICROGLOBULIN
B, E
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
MELANOMA-ASSOCIATED ANTIGEN 1
C, F
9Homo sapiensMutation(s): 0 
Gene Names: MAGEA1 (MAGE1, MAGE1A)
Find proteins for P43355 (Homo sapiens)
Go to Gene View: MAGEA1
Go to UniProtKB:  P43355
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HYB3 HEAVY CHAIN
H, I
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
HYB3 LIGHT CHAIN
L, M
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, I, M
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: 2.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 125.359α = 90.00
b = 50.050β = 109.85
c = 136.705γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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