Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 44.51 kDa 
• Atom Count: 3575 
• Modelled Residue Count: 383 
• Deposited Residue Count: 383 
• Unique protein chains: 3

1T1Z

Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-6A

• PDB DOI: 10.2210/pdb1T1Z/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2004-04-19 Released: 2005-09-06 
• Deposition Author(s): Martinez-Hackert, E., Anikeeva, N., Kalams, S.A., Walker, B.D., Hendrickson, W.A., Sykulev, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Literature

Structural Basis for Degenerate Recognition of Natural HIV Peptide Variants by Cytotoxic Lymphocytes.

Martinez-Hackert, E., Anikeeva, N., Kalams, S.A., Walker, B.D., Hendrickson, W.A., Sykulev, Y.

(2006) J Biol Chem 281: 20205-20212

• PubMed: 16702212 
• DOI: 10.1074/jbc.M601934200
• Primary Citation of Related Structures:  
  1S8D, 1T1W, 1T1X, 1T1Y, 1T1Z, 1T20, 1T21, 1T22


• PubMed Abstract: 
  

It is well established that even small changes in amino acid side chains of antigenic peptide bound to major histocompatibility complex (MHC) protein may completely abrogate recognition of the peptide-MHC (pMHC) complex by the T cell receptor (TCR). Often, however, several nonconservative substitutions in the peptide antigen are accommodated and do not impair its recognition by TCR. For example, a preponderance of natural sequence variants of the human immunodeficiency virus p17 Gag-derived peptide SLYNTVATL (SL9) are recognized by cytotoxic T lymphocytes, which implies that interactions with SL9 variants are degenerate both with respect to the class I MHC molecule and with respect to TCR. Here we study the molecular basis for this degenerate recognition of SL9 variants. We show that several SL9 variants bind comparably well to soluble HLA-A2 and to a particular soluble TCR and that these variants are active in the cognate cytotoxicity assay. Natural SL9 variation is restricted by its context in the HIV p17 matrix protein. High resolution crystal structures of seven selected SL9 variants bound to HLA-A2 all have remarkably similar peptide conformations and side-chain dispositions outside sites of substitution. This preservation of the peptide conformation despite epitope variations suggests a mechanism for the observed degeneracy in pMHC recognition by TCR and may contribute to the persistence of SL9-mediated immune responses in chronically infected individuals.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A	275	Homo sapiens	Mutation(s): 0  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	99	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
GAG PEPTIDE	C	9	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.65	α = 90
b = 78.69	β = 116.22
c = 56.93	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-19 
• Released Date: 2005-09-06 
Deposition Author(s): Martinez-Hackert, E., Anikeeva, N., Kalams, S.A., Walker, B.D., Hendrickson, W.A., Sykulev, Y.

Revision History  

• Version 1.0: 2005-09-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance