Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 91.67 kDa 
• Atom Count: 7,206 
• Modelled Residue Count: 768 
• Deposited Residue Count: 768 
• Unique protein chains: 3

 2AV1

Crystal structure of HTLV-1 TAX peptide Bound to Human Class I MHC HLA-A2 with the E63Q and K66A mutations in the heavy chain.

• PDB DOI:  https://doi.org/10.2210/pdb2AV1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human T-cell lymphotrophic virus type 1 (Caribbean isolate)
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-08-29 Released: 2005-10-18 
• Deposition Author(s): Borbulevych, O.Y., Baker, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.231 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Literature

Unraveling a Hotspot for TCR Recognition on HLA-A2: Evidence Against the Existence of Peptide-independent TCR Binding Determinants.

Gagnon, S.J., Borbulevych, O.Y., Davis-Harrison, R.L., Baxter, T.K., Clemens, J.R., Armstrong, K.M., Turner, R.V., Damirjian, M., Biddison, W.E., Baker, B.M.

(2005) J Mol Biol 353: 556-573

• PubMed: 16197958 
• DOI: https://doi.org/10.1016/j.jmb.2005.08.024
• Primary Citation of Related Structures:  
  2AV1, 2AV7


• PubMed Abstract: 
  

T cell receptor (TCR) recognition of peptide takes place in the context of the major histocompatibility complex (MHC) molecule, which accounts for approximately two-thirds of the peptide/MHC buried surface. Using the class I MHC HLA-A2 and a large panel of mutants, we have previously shown that surface mutations that disrupt TCR recognition vary with the identity of the peptide. The single exception is Lys66 on the HLA-A2 alpha1 helix, which when mutated to alanine disrupts recognition for 93% of over 250 different T cell clones or lines, independent of which peptide is bound. Thus, Lys66 could serve as a peptide-independent TCR binding determinant. Here, we have examined the role of Lys66 in TCR recognition of HLA-A2 in detail. The structure of a peptide/HLA-A2 molecule with the K66A mutation indicates that although the mutation induces no major structural changes, it results in the exposure of a negatively charged glutamate (Glu63) underneath Lys66. Concurrent replacement of Glu63 with glutamine restores TCR binding and function for T cells specific for five different peptides presented by HLA-A2. Thus, the positive charge on Lys66 does not serve to guide all TCRs onto the HLA-A2 molecule in a manner required for productive signaling. Furthermore, electrostatic calculations indicate that Lys66 does not contribute to the stability of two TCR-peptide/HLA-A2 complexes. Our findings are consistent with the notion that each TCR arrives at a unique solution of how to bind a peptide/MHC, most strongly influenced by the chemical and structural features of the bound peptide. This would not rule out an intrinsic affinity of TCRs for MHC molecules achieved through multiple weak interactions, but for HLA-A2 the collective mutational data place limits on the role of any single MHC amino acid side-chain in driving TCR binding in a peptide-independent fashion.

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Organizational Affiliation: 

Molecular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A, D	275	Homo sapiens	Mutation(s): 2  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Trans-activating transcriptional regulatory peptide	C, F	9	Human T-cell lymphotrophic virus type 1 (Caribbean isolate)	Mutation(s): 0  Gene Names: tax
UniProt
Find proteins for P14079 (Human T-cell leukemia virus 1 (isolate Caribbea HS-35 subtype A)) Explore P14079  Go to UniProtKB:  P14079

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AA [auth D], BA [auth E], CA [auth E], DA [auth E], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth C], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN	M [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.231 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.328	α = 82.1
b = 62.536	β = 76.39
c = 74.747	γ = 78.1

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-18 
Deposition Author(s): Borbulevych, O.Y., Baker, B.M.

Revision History  

• Version 1.0: 2005-10-18
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2013-03-13
  Changes: Other
• Version 1.5: 2021-10-20
  Changes: Database references, Derived calculations