Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 45.11 kDa 
• Atom Count: 3738 
• Residue Count: 384 
• Unique protein chains: 3

3L3I

Crystal structure of HLA-B*4402 in complex with the F7A mutant of a self-peptide derived from DPA*0201

• DOI: 10.2210/pdb3L3I/pdb

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


• Deposited: 2009-12-17 Released: 2010-03-16 
• Deposition Author(s): Theodossis, A., Ely, L.K., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.242 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Constraints within major histocompatibility complex class I restricted peptides: presentation and consequences for T-cell recognition

Theodossis, A., Guillonneau, C., Welland, A., Ely, L.K., Clements, C.S., Williamson, N.A., Webb, A.I., Wilce, J.A., Mulder, R.J., Dunstone, M.A., Doherty, P.C., McCluskey, J., Purcell, A.W., Turner, S.J., Rossjohn, J.

(2010) Proc Natl Acad Sci U S A 107: 5534-5539

• PubMed: 20212169 
• DOI: 10.1073/pnas.1000032107
• Primary Citation of Related Structures:  
  3L3J, 3L3K, 3L3D, 3L3G, 3L3H, 3L3I


• PubMed Abstract: 
  

Residues within processed protein fragments bound to major histocompatibility complex class I (MHC-I) glycoproteins have been considered to function as a series of "independent pegs" that either anchor the peptide (p) to the MHC-I and/or interact with the spectrum of alphabeta-T-cell receptors (TCRs) specific for the pMHC-I epitope in question. Mining of the extensive pMHC-I structural database established that many self- and viral peptides show extensive and direct interresidue interactions, an unexpected finding that has led us to the idea of "constrained" peptides. Mutational analysis of two constrained peptides (the HLA B44 restricted self-peptide (B44DPalpha-EEFGRAFSF) and an H2-D(b) restricted influenza peptide (D(b)PA, SSLENFRAYV) demonstrated that the conformation of the prominently exposed arginine in both peptides was governed by interactions with MHC-I-orientated flanking residues from the peptide itself. Using reverse genetics in a murine influenza model, we revealed that mutation of an MHC-I-orientated residue (SSLENFRAYV --> SSLENARAYV) within the constrained PA peptide resulted in a diminished cytotoxic T lymphocyte (CTL) response and the recruitment of a limited pMHC-I specific TCR repertoire. Interactions between individual peptide positions can thus impose fine control on the conformation of pMHC-I epitopes, whereas the perturbation of such constraints can lead to a previously unappreciated mechanism of viral escape.

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Organizational Affiliation: 

The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B-44 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS  P01889 GTEx  ENSG00000234745

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
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide from HLA-DPA1 protein	C	9	N/A	Mutation(s): 1
Find proteins for Q95HB9 (Homo sapiens) Explore Q95HB9  Go to UniProtKB:  Q95HB9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.242 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.782	α = 90
b = 82.329	β = 90
c = 110.337	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-17 
• Released Date: 2010-03-16 
Deposition Author(s): Theodossis, A., Ely, L.K., Rossjohn, J.

Revision History 

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-26
  Changes: Database references