Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report

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: 45.05 kDa 
• Atom Count: 3425 
• Modelled Residue Count: 385 
• Deposited Residue Count: 385 
• Unique protein chains: 3

3KPO

Crystal Structure of HLA B*4403 in complex with EEYLKAWTF, a mimotope

• DOI: 10.2210/pdb3KPO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-16 Released: 2009-12-22 
• Deposition Author(s): Macdonald, W.A., Chen, Z., Gras, S., Archbold, J.K., Tynan, F.E., Clements, C.S., Bharadwaj, M., Kjer-Nielsen, L., Saunders, P.M., Wilce, M.C., Crawford, F., Stadinsky, B., Jackson, D., Brooks, A.G., Purcell, A.W., Kappler, J.W., Burrows, S.R., Rossjohn, J., McCluskey, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

T cell allorecognition via molecular mimicry.

Macdonald, W.A., Chen, Z., Gras, S., Archbold, J.K., Tynan, F.E., Clements, C.S., Bharadwaj, M., Kjer-Nielsen, L., Saunders, P.M., Wilce, M.C., Crawford, F., Stadinsky, B., Jackson, D., Brooks, A.G., Purcell, A.W., Kappler, J.W., Burrows, S.R., Rossjohn, J., McCluskey, J.

(2009) Immunity 31: 897-908

• PubMed: 20064448 
• DOI: 10.1016/j.immuni.2009.09.025
• Primary Citation of Related Structures:  
  3KPL, 3KPM, 3KPN, 3KPO, 3KPP, 3KPQ, 3KPR, 3KPS


• PubMed Abstract: 
  

T cells often alloreact with foreign human leukocyte antigens (HLA). Here we showed the LC13 T cell receptor (TCR), selected for recognition on self-HLA-B( *)0801 bound to a viral peptide, alloreacts with B44 allotypes (HLA-B( *)4402 and HLA-B( *)4405) bound to two different allopeptides. Despite extensive polymorphism between HLA-B( *)0801, HLA-B( *)4402, and HLA-B( *)4405 and the disparate sequences of the viral and allopeptides, the LC13 TCR engaged these peptide-HLA (pHLA) complexes identically, accommodating mimicry of the viral peptide by the allopeptide. The viral and allopeptides adopted similar conformations only after TCR ligation, revealing an induced-fit mechanism of molecular mimicry. The LC13 T cells did not alloreact against HLA-B( *)4403, and the single residue polymorphism between HLA-B( *)4402 and HLA-B( *)4403 affected the plasticity of the allopeptide, revealing that molecular mimicry was associated with TCR specificity. Accordingly, molecular mimicry that is HLA and peptide dependent is a mechanism for human T cell alloreactivity between disparate cognate and allogeneic pHLA complexes.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, DAMA-387C9.2-001, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
PHAROS:  P01889 GTEx:  ENSG00000234745

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	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 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EEYLKAWTF, mimotope peptide	C	9	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.87	α = 90
b = 81.85	β = 90
c = 109.96	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-16 
• Released Date: 2009-12-22 
Deposition Author(s): Macdonald, W.A., Chen, Z., Gras, S., Archbold, J.K., Tynan, F.E., Clements, C.S., Bharadwaj, M., Kjer-Nielsen, L., Saunders, P.M., Wilce, M.C., Crawford, F., Stadinsky, B., Jackson, D., Brooks, A.G., Purcell, A.W., Kappler, J.W., Burrows, S.R., Rossjohn, J., McCluskey, J.

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance