7N19 | pdb_00007n19

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

PDB DOI: https://doi.org/10.2210/pdb7N19/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, synthetic construct
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2021-05-27 Released: 2021-08-18
Deposition Author(s): Wang, Y., Dai, S.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.248 (Depositor), 0.251 (DCC)
R-Value Work:
0.200 (Depositor), 0.205 (DCC)
R-Value Observed:
0.203 (Depositor)

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 Medicine 218

PubMed: 34410304 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1084/jem.20210785
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 182.49 kDa
Atom Count: 12,988
Modeled Residue Count: 1,516
Deposited Residue Count: 1,536
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A, D, G, J	181	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRA, HLA-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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01903
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain D Focus chain G Focus chain J	Go to GlyGen: P01903-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen DR beta chain	B, E, H, K	189	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRB1, RP1-93N13.1-001
UniProt
Find proteins for Q5Y7D1 (Homo sapiens) Explore Q5Y7D1 Go to UniProtKB: Q5Y7D1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5Y7D1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain H Focus chain K
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HST4 peptide	C, F, I, L	14	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, N, O, P	2		N-Glycosylation	Interactions Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain M Focus chain N Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain HA [auth H] SDF format, chain WA [auth K] SDF format, chain X [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain HA [auth H] MOL2 format, chain WA [auth K] MOL2 format, chain X [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain HA [auth H] mmCIF format, chain WA [auth K] mmCIF format, chain X [auth B]	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		Interactions Focus chain BA [auth D] Focus chain HA [auth H] Focus chain WA [auth K] Focus chain X [auth B] Interactions & Density Focus chain BA [auth D] Focus chain HA [auth H] Focus chain WA [auth K] Focus chain X [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain GA [auth E] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain MA [auth I] SDF format, chain NA [auth I] SDF format, chain OA [auth J] SDF format, chain PA [auth J] SDF format, chain Q [auth A] SDF format, chain QA [auth K] SDF format, chain R [auth B] SDF format, chain RA [auth K] SDF format, chain S [auth B] SDF format, chain SA [auth K] SDF format, chain T [auth B] SDF format, chain TA [auth K] SDF format, chain V [auth B] SDF format, chain VA [auth K] SDF format, chain W [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain XA [auth L] SDF format, chain UA [auth K] SDF format, chain U [auth B] SDF format, chain FA [auth E] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain NA [auth I] MOL2 format, chain OA [auth J] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth K] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth K] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth K] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth K] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth K] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain XA [auth L] MOL2 format, chain UA [auth K] MOL2 format, chain U [auth B] MOL2 format, chain FA [auth E] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain LA [auth H] mmCIF format, chain MA [auth I] mmCIF format, chain NA [auth I] mmCIF format, chain OA [auth J] mmCIF format, chain PA [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth K] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth K] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth K] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth K] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth K] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain XA [auth L] mmCIF format, chain UA [auth K] mmCIF format, chain U [auth B] mmCIF format, chain FA [auth E]	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		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth A] Focus chain QA [auth K] Focus chain R [auth B] Focus chain RA [auth K] Focus chain S [auth B] Focus chain SA [auth K] Focus chain T [auth B] Focus chain TA [auth K] Focus chain U [auth B] Focus chain UA [auth K] Focus chain V [auth B] Focus chain VA [auth K] Focus chain W [auth B] Focus chain XA [auth L] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth A] Focus chain QA [auth K] Focus chain R [auth B] Focus chain RA [auth K] Focus chain S [auth B] Focus chain SA [auth K] Focus chain T [auth B] Focus chain TA [auth K] Focus chain U [auth B] Focus chain UA [auth K] Focus chain V [auth B] Focus chain VA [auth K] Focus chain W [auth B] Focus chain XA [auth L] Focus chain Y [auth C] Focus chain Z [auth C]