2Z35 | pdb_00002z35

Crystal structure of immune receptor

• PDB DOI: https://doi.org/10.2210/pdb2Z35/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-01 Released: 2007-10-09 
• Deposition Author(s): Feng, D., Bond, C.J., Ely, L.K., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.285 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.271 (DCC) 

Literature

Structural evidence for a germline-encoded T cell receptor-major histocompatibility complex interaction 'codon'

Feng, D., Bond, C.J., Ely, L.K., Maynard, J., Garcia, K.C.

(2007) Nat Immunol 8: 975-983

• PubMed: 17694060 
• DOI: https://doi.org/10.1038/ni1502
• Primary Citation Related Structures: 
  2PXY, 2Z31, 2Z35


• PubMed Abstract: 
  

  All complexes of T cell receptors (TCRs) bound to peptide-major histocompatibility complex (pMHC) molecules assume a stereotyped binding 'polarity', despite wide variations in TCR-pMHC docking angles. However, existing TCR-pMHC crystal structures have failed to show broadly conserved pairwise interaction motifs. Here we determined the crystal structures of two TCRs encoded by the variable beta-chain 8.2 (V(beta)8.2), each bound to the MHC class II molecule I-A(u), and did energetic mapping of V(alpha) and V(beta) contacts with I-A(u). Together with two previously solved structures of V(beta)8.2-containing TCR-MHC complexes, we found four TCR-I-A complexes with structurally superimposable interactions between the V(beta) loops and the I-A alpha-helix. This examination of a narrow 'slice' of the TCR-MHC repertoire demonstrates what is probably one of many germline-derived TCR-MHC interaction 'codons'.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.48 kDa 
• Atom Count: 1,751 
• Modeled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor alpha-chain	A	112	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q5R1F5 (Mus musculus) Explore Q5R1F5  Go to UniProtKB:  Q5R1F5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor beta-chain	B	111	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A2NTY6 (Mus musculus) Explore A2NTY6  Go to UniProtKB:  A2NTY6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.285 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.271 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.994	α = 90
b = 73.802	β = 90
c = 115.374	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Feng, D., Bond, C.J., Ely, L.K., Garcia, K.C.

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary