Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1BCD 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1BCD 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 182.09 kDa 
• Atom Count: 13471 
• Residue Count: 1632 
• Unique protein chains: 5

1W72

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

• DOI: 10.2210/pdb1W72/pdb

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


• Deposited: 2004-08-27 Released: 2004-11-09 
• Deposition Author(s): 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.

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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 

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

• PubMed: 15537658 
• DOI: 10.1074/jbc.M411323200
• Structures With Same Primary Citation


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN	A, D	274	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
BETA-2-MICROGLOBULIN	B, E	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
MELANOMA-ASSOCIATED ANTIGEN 1	C, F	9	Homo sapiens	Mutation(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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
HYB3 HEAVY CHAIN	H, I	223	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
HYB3 LIGHT CHAIN	L, M	210	Homo sapiens	Mutation(s): 0

Small Molecules

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

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 = 125.359	α = 90
b = 50.05	β = 109.85
c = 136.705	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-27 
• Released Date: 2004-11-09 
Deposition Author(s): 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.

Revision History 

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