Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.17 kDa 
• Atom Count: 3606 
• Residue Count: 386 
• Unique protein chains: 3

5NI9

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

• DOI: 10.2210/pdb5NI9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-23 Released: 2018-06-13 
• Deposition Author(s): Gerstner, C., Dubnovitsky, A.

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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 

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

• PubMed: 29853344 
• DOI: 10.1016/j.jaut.2018.04.004
• Primary Citation of Related Structures:  
  5NIG, 5NI9


• 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. 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.

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Organizational Affiliation: 

Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A	189	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903 GTEx  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DRB1-4 beta chain	B	198	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS  P01911 GTEx  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-enolase	C	15	Homo sapiens	Mutation(s): 0  Gene Names: ENO1, ENO1L1, MBPB1, MPB1 EC: 4.2.1.11
Find proteins for P06733 (Homo sapiens) Explore P06733  Go to UniProtKB:  P06733
NIH Common Fund Data Resources
PHAROS  P06733 GTEx  ENSG00000074800

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	A	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	B, C	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
URE	A, B	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N

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 = 68.447	α = 90
b = 128.109	β = 90
c = 53.585	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-23 
• Released Date: 2018-06-13 
Deposition Author(s): Gerstner, C., Dubnovitsky, A.

Revision History 

• 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