Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 47074.38 
• Atom Count: 3453 
• Residue Count: 402 
• Unique protein chains: 3

3MRG

Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide

• DOI: 10.2210/pdb3MRG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Hepatitis C virus genotype 1b
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2010-04-29 Released: 2011-05-25 
• Deposition Author(s): Gras, S., Reiser, J.-B., Echasserieau, K., Saulquin, X., Bonneville, M., Housset, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.202 
• R-Value Work: 0.179 

Literature

Analysis of Relationships between Peptide/MHC Structural Features and Naive T Cell Frequency in Humans.

Reiser, J.B., Legoux, F., Gras, S., Trudel, E., Chouquet, A., Leger, A., Le Gorrec, M., Machillot, P., Bonneville, M., Saulquin, X., Housset, D.

(2014) J.Immunol. 193: 5816-5826

• PubMed: 25392532 
• DOI: 10.4049/jimmunol.1303084
• Primary Citation of Related Structures:  
  3MRR, 3MRO, 3MRL, 3MRH, 3MRE, 3MRD, 3MRC


• PubMed Abstract: 
  

The structural rules governing peptide/MHC (pMHC) recognition by T cells remain unclear. To address this question, we performed a structural characterization of several HLA-A2/peptide complexes and assessed in parallel their antigenicity, by analyzing the frequency of the corresponding Ag-specific naive T cells in A2(+) and A2(-) individuals, as well as within CD4(+) and CD8(+) subsets. We were able to find a correlation between specific naive T cell frequency and peptide solvent accessibility and/or mobility for a subset of moderately prominent peptides. However, one single structural parameter of the pMHC complexes could not be identified to explain each peptide antigenicity. Enhanced pMHC antigenicity was associated with both highly biased TRAV usage, possibly reflecting favored interaction between particular pMHC complexes and germline TRAV loops, and peptide structural features allowing interactions with a broad range of permissive CDR3 loops. In this context of constrained TCR docking mode, an optimal peptide solvent exposed surface leading to an optimal complementarity with TCR interface may constitute one of the key features leading to high frequency of specific T cells. Altogether our results suggest that frequency of specific T cells depends on the fine-tuning of several parameters, the structural determinants governing TCR-pMHC interaction being just one of them.

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Organizational Affiliation: 

Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France;

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	293	Homo sapiens	Mutation(s): 1  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
9-meric peptide from Serine protease/NTPase/helicase NS3	P	9	Hepatitis C virus genotype 1b	Mutation(s): 0
Find proteins for Q03463 (Hepatitis C virus genotype 1b) Go to UniProtKB:  Q03463

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CIT	A	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.202 
• R-Value Work: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 53.120	α = 90.00
b = 80.870	β = 112.33
c = 56.200	γ = 90.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-29 
• Released Date: 2011-05-25 
• Deposition Author(s): Gras, S., Reiser, J.-B., Echasserieau, K., Saulquin, X., Bonneville, M., Housset, D.

Revision History 

• Version 1.0: 2011-05-25
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2015-01-28
  Type: Database references