Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 96013.35 
• Atom Count: 6740 
• Residue Count: 822 
• Unique protein chains: 5

2PYE

Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry TCR Clone C5C1 Complexed with MHC

• DOI: 10.2210/pdb2PYE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2007-05-16 Released: 2007-09-25 
• Deposition Author(s): Sami, M., Rizkallah, P.J., Dunn, S., Li, Y., Moysey, R., Vuidepot, A., Baston, E., Todorov, P., Molloy, P., Gao, F., Boulter, J.M., Jakobsen, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.283 
• R-Value Work: 0.192 

Literature

Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry

Sami, M., Rizkallah, P.J., Dunn, S., Molloy, P., Moysey, R., Vuidepot, A., Baston, E., Todorov, P., Yi, L., Gao, F., Boulter, J.M., Jakobsen, B.K.

(2007) Protein Eng.Des.Sel. 20: 397-403

• PubMed: 17644531 
• DOI: 10.1093/protein/gzm033
• Primary Citation of Related Structures:  
  2PYF, 2P5W, 2P5E


• PubMed Abstract: 
  

Naturally selected T-cell receptors (TCRs) are characterised by low binding affinities, typically in the range 1-100 microM. Crystal structures of syngeneic TCRs bound to peptide major histocompatibility complex (pMHC) antigens exhibit a conserved mode of binding characterised by a distinct diagonal binding geometry, with poor shape complementarity (SC) between receptor and ligand. Here, we report the structures of three in vitro affinity enhanced TCRs that recognise the pMHC tumour epitope NY-ESO(157-165) (SLLMWITQC). These crystal structures reveal that the docking mode for the high affinity TCRs is identical to that reported for the parental wild-type TCR, with only subtle changes in the mutated complementarity determining regions (CDRs) that form contacts with pMHC; both CDR2 and CDR3 mutations act synergistically to improve the overall affinity. Comparison of free and bound TCR structures for both wild-type and a CDR3 mutant reveal an induced fit mechanism arising from restructuring of CDR3 loops which allows better peptide binding. Overall, an increased interface area, improved SC and additional H-bonding interactions are observed, accounting for the increase in affinity. Most notably, there is a marked increase in the SC for the central methionine and tryptophan peptide motif over the native TCR.

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Organizational Affiliation: 

Avidex Limited (subsidiary of Medigene Ag), 57c Milton Park, Abingdon, Oxon OX14 4RX, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class I histocompatibility antigen, A-2 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A (HLAA)
Find proteins for P01892 (Homo sapiens) Go to Gene View: HLA-A Go to UniProtKB:  P01892

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Cancer/testis antigen 1B	C	9	Homo sapiens	Mutation(s): 0  Gene Names: CTAG1A, CTAG1B (CTAG, CTAG1, ESO1, LAGE2, LAGE2A, LAGE2B)
Find proteins for P78358 (Homo sapiens) Go to Gene View: CTAG1A CTAG1B Go to UniProtKB:  P78358

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
T-Cell Receptor, Alpha Chain	D	195	Homo sapiens	Mutation(s): 0  Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens) Go to UniProtKB:  P01848

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
T-Cell Receptor, Beta Chain	E	242	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, D, E	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B, D, E	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
7PE	A	2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL POLYETHYLENE GLYCOL FRAGMENT C14 H30 O7 UKXKPKBTMYNOFS-UHFFFAOYSA-N
PGE	A, E	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.283 
• R-Value Work: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 74.752	α = 90.00
b = 52.907	β = 97.94
c = 119.904	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOSFLM	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-16 
• Released Date: 2007-09-25 
• Deposition Author(s): Sami, M., Rizkallah, P.J., Dunn, S., Li, Y., Moysey, R., Vuidepot, A., Baston, E., Todorov, P., Molloy, P., Gao, F., Boulter, J.M., Jakobsen, B.K.

Revision History 

• Version 1.0: 2007-09-25
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Derived calculations, Version format compliance