7T2A

Crystal structure of HLA-DP4 in complex with Ply


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

CD4 + T cell-mediated recognition of a conserved cholesterol-dependent cytolysin epitope generates broad antibacterial immunity.

Ciacchi, L.van de Garde, M.D.B.Ladell, K.Farenc, C.Poelen, M.C.M.Miners, K.L.Llerena, C.Reid, H.H.Petersen, J.Price, D.A.Rossjohn, J.van Els, C.A.C.M.

(2023) Immunity 56: 1082-1097.e6

  • DOI: https://doi.org/10.1016/j.immuni.2023.03.020
  • Primary Citation of Related Structures:  
    7T2A, 7T2B, 7T2C, 7T2D

  • PubMed Abstract: 

    CD4 + T cell-mediated immunity against Streptococcus pneumoniae (pneumococcus) can protect against recurrent bacterial colonization and invasive pneumococcal diseases (IPDs). Although such immune responses are common, the pertinent antigens have remained elusive. We identified an immunodominant CD4 + T cell epitope derived from pneumolysin (Ply), a member of the bacterial cholesterol-dependent cytolysins (CDCs). This epitope was broadly immunogenic as a consequence of presentation by the pervasive human leukocyte antigen (HLA) allotypes DPB1 02 and DPB1 04 and recognition via architecturally diverse T cell receptors (TCRs). Moreover, the immunogenicity of Ply 427-444 was underpinned by core residues in the conserved undecapeptide region (ECTGLAWEWWR), enabling cross-recognition of heterologous bacterial pathogens expressing CDCs. Molecular studies further showed that HLA-DP4-Ply 427-441 was engaged similarly by private and public TCRs. Collectively, these findings reveal the mechanistic determinants of near-global immune focusing on a trans-phyla bacterial epitope, which could inform ancillary strategies to combat various life-threatening infectious diseases, including IPDs.


  • Organizational Affiliation

    Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DP alpha 1 chain
A, D
181Homo sapiensMutation(s): 0 
Gene Names: HLA-DPA1HLA-DP1AHLASB
UniProt & NIH Common Fund Data Resources
Find proteins for P20036 (Homo sapiens)
Explore P20036 
Go to UniProtKB:  P20036
PHAROS:  P20036
GTEx:  ENSG00000231389 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20036
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DP beta 1 chain
B, E
188Homo sapiensMutation(s): 0 
Gene Names: HLA-DPB1HLA-DP1B
UniProt & NIH Common Fund Data Resources
Find proteins for P04440 (Homo sapiens)
Explore P04440 
Go to UniProtKB:  P04440
PHAROS:  P04440
GTEx:  ENSG00000223865 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04440
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pneumolysin-derived peptide
C, F
15Streptococcus pneumoniaeMutation(s): 0 
Gene Names: plySPD_1726
UniProt
Find proteins for Q04IN8 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466))
Explore Q04IN8 
Go to UniProtKB:  Q04IN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04IN8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.669α = 90
b = 101.669β = 90
c = 215.187γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description