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 

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:  

  • 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 <sub>326-340 </sub> in the context of HLA ...

    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

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Chemistry, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany.,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, China.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA.,Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,College of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.,Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,DISFARM, Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi, Milano, Italy.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, 50674 Koeln, Germany.,Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.,Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France.,Pfizer Worldwide Research & Development , 610 Main Street, Cambridge, Massachusetts 02139, United States.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada. john.pascal@umontreal.ca.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA. blackbe@pennmedicine.upenn.edu.,Tetramer Core, BRI at Virginia Mason, Seattle, WA, USA.,Translational Research Program, BRI at Virginia Mason, Seattle, WA, USA.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: Vivianne.malmstrom@ki.se.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DRB1-4 beta chain
B
198Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P13760 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P13760
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Alpha-enolase
C
15Homo sapiensMutation(s): 0 
Gene Names: ENO1 (ENO1L1, MBPB1, MPB1)
EC: 4.2.1.11
Find proteins for P06733 (Homo sapiens)
Go to Gene View: ENO1
Go to UniProtKB:  P06733
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
URE
Query on URE

Download SDF File 
Download CCD File 
A, B
UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
B, C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-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 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.447α = 90.00
b = 128.109β = 90.00
c = 53.585γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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