PXD014253

PXD014253 is an original dataset announced via ProteomeXchange.

Title	The HLA-DRB1*03:01 ligandome is highly conserved on N- and C-terminal residues outside the peptide-binding cleft
Description	Human CD4+ T lymphocytes play an important role in inducing potent immune responses. They are activated and stimulated by peptides presented in Major Histocompatibility Complex Class II molecules. These MHC class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the MHC molecule, designated as the binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different types of cells , the ligandomes of HLA-DRB1*03:01 derived from two different cell types (dendritic cells and EBV-transformed B-cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, these terminal conservations of the HLA-DRB1*03:01 ligandome were compared to the N- and C-terminal conservations of the HLA-DRB1*04:01 ligandome acquired from dendritic cells. Again, comparable conservations were evident with only minor differences. Taken all together, these analyses show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.
HostingRepository	PRIDE
AnnounceDate	2019-09-25
AnnouncementXML	Submission_2019-09-25_11:16:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	G Janssen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-13 07:04:25	ID requested
⏵ 1	2019-09-25 11:16:49	announced

Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM, Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft. Immunogenetics, 71(8-9):519-530(2019) [pubmed]

submitter keyword: DUCAF

HLA-DRB1*03:01

Peter A van Veelen
contact affiliation	LUMC Head Proteomics group Centre for Proteomics and Metabolomics LUMC
contact email	p.a.van_veelen@lumc.nl
lab head
G Janssen
contact affiliation	Leiden University Medical Center
contact email	g.m.c.janssen@lumc.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD014253
     1. Label: PRIDE project
     2. Name: The HLA-DRB1*03:01 ligandome is highly conserved on N- and C-terminal residues outside the peptide-binding cleft