5NI9

Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Memory T cells specific to citrullinated alpha-enolase are enriched in the rheumatic joint.

Pieper, J., Dubnovitsky, A., Gerstner, C., James, E.A., Rieck, M., Kozhukh, G., Tandre, K., Pellegrino, S., Gebe, J.A., Ronnblom, L., Sandalova, T., Kwok, W.W., Klareskog, L., Buckner, J.H., Achour, A., Malmstrom, V.

(2018) J Autoimmun 92: 47-56

  • DOI: 10.1016/j.jaut.2018.04.004
  • Primary Citation of Related Structures:  
    5NI9, 5NIG

  • PubMed Abstract: 

    • ACPA-positive rheumatoid arthritis (RA) is associated with distinct HLA-DR alleles and immune responses to many citrullinated self-antigens. Herein we investigated the T cell epitope confined within α-enolase 326-340 in the context of HLA-DRB1*04:01 and assessed the corresponding CD4 + T cells in both the circulation and in the rheumatic joint ...

    ACPA-positive rheumatoid arthritis (RA) is associated with distinct HLA-DR alleles and immune responses to many citrullinated self-antigens. Herein we investigated the T cell epitope confined within α-enolase 326-340 in the context of HLA-DRB1*04:01 and assessed the corresponding CD4 + T cells in both the circulation and in the rheumatic joint. Comparative crystallographic analyses were performed for the native and citrullinated α-enolase 326-340 peptides in complex with HLA-DRB1*04:01. HLA-tetramers assembled with either the native or citrullinated peptide were used for ex vivo and in vitro assessment of α-enolase-specific T cells in peripheral blood, synovial fluid and synovial tissue by flow cytometry. The native and modified peptides take a completely conserved structural conformation within the peptide-binding cleft of HLA-DRB1*04:01. The citrulline residue-327 was located N-terminally, protruding towards TCRs. The frequencies of T cells recognizing native eno 326-340 were similar in synovial fluid and peripheral blood, while in contrast, the frequency of T cells recognizing cit-eno 326-340 was significantly elevated in synovial fluid compared to peripheral blood (3.6-fold, p = 0.0150). Additionally, citrulline-specific T cells with a memory phenotype were also significantly increased (1.6-fold, p = 0.0052) in synovial fluid compared to peripheral blood. The native T cell epitope confined within α-enolase 326-340 does not appear to lead to complete negative selection of cognate CD4 + T cells. In RA patient samples, only T cells recognizing the citrullinated version of α-enolase 326-340 were found at elevated frequencies implicating that neo-antigen formation is critical for breach of tolerance.

    Organizational Affiliation: 

    Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: Vivianne.malmstrom@ki.se.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
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Find proteins for P01903 (Homo sapiens)
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PHAROS:  P01903
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UniProt GroupP01903
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-4 beta chainB198Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
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Find proteins for P01911 (Homo sapiens)
Explore P01911 
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PHAROS:  P01911
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UniProt GroupP01911
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-enolaseC15Homo sapiensMutation(s): 0 
Gene Names: ENO1, ENO1L1, MBPB1, MPB1
EC: 4.2.1.11
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Find proteins for P06733 (Homo sapiens)
Explore P06733 
Go to UniProtKB:  P06733
PHAROS:  P06733
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UniProt GroupP06733
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
Download Ideal Coordinates CCD File 
F [auth B],
H [auth C]		(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
MRD
Query on MRD
Download Ideal Coordinates CCD File 
D [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N		 Ligand Interaction
URE
Query on URE
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.447α = 90
b = 128.109β = 90
c = 53.585γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection