2BCK

Crystal Structure of HLA-A*2402 Complexed with a telomerase peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of HLA-A*2402 complexed with a telomerase peptide.

Cole, D.K.Rizkallah, P.J.Gao, F.Watson, N.I.Boulter, J.M.Bell, J.I.Sami, M.Gao, G.F.Jakobsen, B.K.

(2006) Eur J Immunol 36: 170-179

  • DOI: 10.1002/eji.200535424
  • Primary Citation of Related Structures:  
    2BCK

  • PubMed Abstract: 
  • HLA-A*2402 is the most commonly expressed HLA allele in oriental populations. It is also widely expressed in the Caucasian population, making it one of, if not the most abundant HLA I types. In order to study its structure in terms of overall fold and peptide presentation, a soluble form of this HLA I (alpha1, alpha2, alpha3 and beta(2)m domains) has been expressed, refolded and crystallized in complex with a cancer-related telomerase peptide (VYGFVRACL), and its structure has been solved to 2 ...

    HLA-A*2402 is the most commonly expressed HLA allele in oriental populations. It is also widely expressed in the Caucasian population, making it one of, if not the most abundant HLA I types. In order to study its structure in terms of overall fold and peptide presentation, a soluble form of this HLA I (alpha1, alpha2, alpha3 and beta(2)m domains) has been expressed, refolded and crystallized in complex with a cancer-related telomerase peptide (VYGFVRACL), and its structure has been solved to 2.8 A resolution. The overall structure of HLA-A*2402 is virtually identical to other reported peptide-HLA I structures. However, there are distinct features observable from this structure at the HLA I peptide binding pockets. The size and depth of pocket B makes it highly suitable for binding to large aromatic side chains, which explains the high prevalence of tyrosine at peptide position 2. Also, for HLA binding at peptide position 5, there is an additional anchor point, which allows the proximal amino acids to protrude out, providing a prominent feature for TCR interaction. Finally, pocket F allows the anchor residue at position 9 to be bound unusually deeply within the HLA structure.


    Organizational Affiliation

    Nuffield Dept. of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-24 alpha chainA, D294Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
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Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
PHAROS:  P04439
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Telomerase reverse transcriptaseC, F9N/AMutation(s): 0 
EC: 2.7.7.49
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Find proteins for O14746 (Homo sapiens)
Explore O14746 
Go to UniProtKB:  O14746
PHAROS:  O14746
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.505α = 90
b = 132.186β = 128.8
c = 91.197γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance