7N19

DR3 in complex with Aspergillus nidulans NAD-dependent histone deacetylase hst4 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

CD4+ T cells in the lungs of acute sarcoidosis patients recognize an Aspergillus nidulans epitope.

Greaves, S.A.Ravindran, A.Santos, R.G.Chen, L.Falta, M.T.Wang, Y.Mitchell, A.M.Atif, S.M.Mack, D.G.Tinega, A.N.Maier, L.A.Dai, S.Pinilla, C.Grunewald, J.Fontenot, A.P.

(2021) J Exp Med 218

  • DOI: https://doi.org/10.1084/jem.20210785
  • Primary Citation of Related Structures:  
    7N19

  • PubMed Abstract: 

    Löfgren's syndrome (LS) is an acute form of sarcoidosis characterized by a genetic association with HLA-DRB1*03 (HLA-DR3) and an accumulation of CD4+ T cells of unknown specificity in the bronchoalveolar lavage (BAL). Here, we screened related LS-specific TCRs for antigen specificity and identified a peptide derived from NAD-dependent histone deacetylase hst4 (NDPD) of Aspergillus nidulans that stimulated these CD4+ T cells in an HLA-DR3-restricted manner. Using ELISPOT analysis, a greater number of IFN-γ- and IL-2-secreting T cells in the BAL of DR3+ LS subjects compared with DR3+ control subjects was observed in response to the NDPD peptide. Finally, increased IgG antibody responses to A. nidulans NDPD were detected in the serum of DR3+ LS subjects. Thus, our findings identify a ligand for CD4+ T cells derived from the lungs of LS patients and suggest a role of A. nidulans in the etiology of LS.


  • Organizational Affiliation

    Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain
A, D, G, J
181Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01903
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01903-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen DR beta chain
B, E, H, K
189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1RP1-93N13.1-001
UniProt
Find proteins for Q5Y7D1 (Homo sapiens)
Explore Q5Y7D1 
Go to UniProtKB:  Q5Y7D1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5Y7D1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HST4 peptide
C, F, I, L
14synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, N, O, P
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth D],
HA [auth H],
WA [auth K],
X [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth E]
DA [auth E]
EA [auth E]
FA [auth E]
AA [auth D],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth E],
IA [auth H],
JA [auth H],
KA [auth H],
LA [auth H],
MA [auth I],
NA [auth I],
OA [auth J],
PA [auth J],
Q [auth A],
QA [auth K],
R [auth B],
RA [auth K],
S [auth B],
SA [auth K],
T [auth B],
TA [auth K],
U [auth B],
UA [auth K],
V [auth B],
VA [auth K],
W [auth B],
XA [auth L],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.461α = 90
b = 214.255β = 98.956
c = 74.554γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1R01ES025797-01

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary