PDBsum entry 3gjf

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Immune system PDB id
Protein chains
276 a.a. *
100 a.a. *
206 a.a. *
220 a.a. *
Waters ×1603
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Rational development of high-affinity t-cell receptor-like antibodies
Structure: Hla class i histocompatibility antigen, a-2 alpha chain. Chain: a, d. Fragment: unp residues 25-300. Synonym: mhc class i antigen a 2. Engineered: yes. Beta-2-microglobulin. Chain: b, e. Synonym: beta-2-microglobulin form pi 5.3.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: peptide from human tumours.
1.90Å     R-factor:   0.204     R-free:   0.251
Authors: G.Stewart-Jones,A.Wadle,A.Hombach,E.Shenderov,G.Held, E.Fischer,S.Kleber,F.Stenner-Liewen,S.Bauer,A.Mcmichael, A.Knuth,H.Abken,A.A.Hombach,V.Cerundolo,E.Y.Jones,C.Renner
Key ref:
G.Stewart-Jones et al. (2009). Rational development of high-affinity T-cell receptor-like antibodies. Proc Natl Acad Sci U S A, 106, 5784-5788. PubMed id: 19307587 DOI: 10.1073/pnas.0901425106
08-Mar-09     Release date:   28-Apr-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P01892  (1A02_HUMAN) -  HLA class I histocompatibility antigen, A-2 alpha chain
365 a.a.
276 a.a.
Protein chains
Pfam   ArchSchema ?
P61769  (B2MG_HUMAN) -  Beta-2-microglobulin
119 a.a.
100 a.a.*
Protein chains
No UniProt id for this chain
Struc: 206 a.a.
Protein chains
No UniProt id for this chain
Struc: 220 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   15 terms 
  Biological process     immune system process   21 terms 
  Biochemical function     protein binding     3 terms  


DOI no: 10.1073/pnas.0901425106 Proc Natl Acad Sci U S A 106:5784-5788 (2009)
PubMed id: 19307587  
Rational development of high-affinity T-cell receptor-like antibodies.
G.Stewart-Jones, A.Wadle, A.Hombach, E.Shenderov, G.Held, E.Fischer, S.Kleber, F.Stenner-Liewen, S.Bauer, A.McMichael, A.Knuth, H.Abken, A.A.Hombach, V.Cerundolo, E.Y.Jones, C.Renner.
T-cell interaction with a target cell is a key event in the adaptive immune response and primarily driven by T-cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes. TCR avidity for a given pMHC is determined by number of MHC molecules, availability of coreceptors, and TCR affinity for MHC or peptide, respectively, with peptide recognition being the most important factor to confer target specificity. Here we present high-resolution crystal structures of 2 Fab antibodies in complex with the immunodominant NY-ESO-1(157-165) peptide analogue (SLLMWITQV) presented by HLA-A*0201 and compare them with a TCR recognizing the same pMHC. Binding to the central methionine-tryptophan peptide motif and orientation of binding were almost identical for Fabs and TCR. As the MW "peg" dominates the contacts between Fab and peptide, we estimated the contributions of individual amino acids between the Fab and peptide to provide the rational basis for a peptide-focused second-generation, high-affinity antibody library. The final Fab candidate achieved better peptide binding by 2 light-chain mutations, giving a 20-fold affinity improvement to 2-4 nM, exceeding the affinity of the TCR by 1,000-fold. The high-affinity Fab when grafted as recombinant TCR on T cells conferred specific killing of HLA-A*0201/NY-ESO-1(157-165) target cells. In summary, we prove that affinity maturation of antibodies mimicking a TCR is possible and provide a strategy for engineering high-affinity antibodies that can be used in targeting specific pMHC complexes for diagnostic and therapeutic purposes.
  Selected figure(s)  
Figure 1.
Structural comparison of TCR and Fab. (A) Comparison of positions of 1G4 TCR (red) and 3M4E5 Fab in complex with HLA-A*0201/NY-ESO-1[157–167]. (B) Positions of the CDR3 loops (blue and magenta) bound to the peptide (cyan) and MHC (gray), and the 2 positions of the CDR2 VH loop from the 3M4F4 complex in the up (red) and down conformations. (C) Schematic of CDR loops of 1G4 TCR in complex with HLA-A*0201/NY-ESO-1[157–167] with loops colored as follows: Vα CDR1, green; Vα CDR2, red; Vα CDR3, blue; Vβ CDR1, magenta; Vβ CDR2, orange; and Vβ CDR3, cyan. Water molecules within 4 Å of both TCR and peptide are indicated as red spheres. (D) Diagram of CDR loops of 3M4E5 Fab in complex with HLA- A*0201/NYESO-1[157–167] with loops colored as follows: VH CDR1, green; VH CDR2, red; VH CDR3, blue; VL CDR1, magenta; VL CDR2, orange; and VL CDR3, cyan. Water molecules within 4 Å of both TCR and peptide are indicated as red spheres. (E) Structure of the 1G4 TCR residues forming the “roof” residues in the cavity that binds the peptide (cyan) MW side chains. (F) The analogous 3M4E5 Fab side chains that form the peptide MW binding cavity. Hydrogen bonds are shown in black dashed lines.
Figure 2.
Structural basis for a second-generation library. (A) Side view of 3M4E5 Fab in complex with HLA-A*0201/NY-ESO-1[157–167], with residues randomized in the second-generation phage display library highlighted as spheres. Colors are as in Fig. 1D. (B–D) Illustrations of 3M4E5 Fab CDR residues that were randomized (red) in the vicinity of the peptide, which displayed nonoptimal contacts with the peptide. Residues making key contacts with the peptide MW side chains and lining the cavity in the CDR loops that interacts with the MW peg are colored in blue. The NYESO-1[157–167] peptide is colored cyan, and hydrogen bonds are represented as dashed black lines.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21296998 A.Sergeeva, G.Alatrash, H.He, K.Ruisaard, S.Lu, J.Wygant, B.W.McIntyre, Q.Ma, D.Li, L.St John, K.Clise-Dwyer, and J.J.Molldrem (2011).
An anti-PR1/HLA-A2 T-cell receptor-like antibody mediates complement-dependent cytotoxicity against acute myeloid leukemia progenitor cells.
  Blood, 117, 4262-4272.  
21364947 J.M.Khan, and S.Ranganathan (2011).
Understanding TR Binding to pMHC Complexes: How Does a TR Scan Many pMHC Complexes yet Preferentially Bind to One.
  PLoS One, 6, e17194.  
20448573 M.Brenner (2010).
T cell receptors and cancer: gain gives pain.
  Nat Med, 16, 520-521.  
20467460 M.Cartellieri, M.Bachmann, A.Feldmann, C.Bippes, S.Stamova, R.Wehner, A.Temme, and M.Schmitz (2010).
Chimeric antigen receptor-engineered T cells for immunotherapy of cancer.
  J Biomed Biotechnol, 2010, 956304.  
20663186 Y.Nakamura, T.Komiyama, M.Furue, T.Gojobori, and Y.Akiyama (2010).
CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies.
  BMC Bioinformatics, 11, 398.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.