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 2LRI | pdb_00002lri

NMR structure of the second PHD finger of AIRE (AIRE-PHD2)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 50 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 2LRI

This is version 1.3 of the entry. See complete history. 

Literature

AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome.

Gaetani, M., Matafora, V., Saare, M., Spiliotopoulos, D., Mollica, L., Quilici, G., Chignola, F., Mannella, V., Zucchelli, C., Peterson, P., Bachi, A., Musco, G.

(2012) Nucleic Acids Res 40: 11756-11768

  • DOI: https://doi.org/10.1093/nar/gks933
  • Primary Citation Related Structures: 
    2LRI

  • PubMed Abstract: 

    Mutations in autoimmune regulator (AIRE) gene cause autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. AIRE is expressed in thymic medullary epithelial cells, where it promotes the expression of peripheral-tissue antigens to mediate deletional tolerance, thereby preventing self-reactivity. AIRE contains two plant homeodomains (PHDs) which are sites of pathological mutations. AIRE-PHD fingers are important for AIRE transcriptional activity and presumably play a crucial role in the formation of multimeric protein complexes at chromatin level which ultimately control immunological tolerance. As a step forward the understanding of AIRE-PHD fingers in normal and pathological conditions, we investigated their structure and used a proteomic SILAC approach to assess the impact of patient mutations targeting AIRE-PHD fingers. Importantly, both AIRE-PHD fingers are structurally independent and mutually non-interacting domains. In contrast to D297A and V301M on AIRE-PHD1, the C446G mutation on AIRE-PHD2 destroys the structural fold, thus causing aberrant AIRE localization and reduction of AIRE target genes activation. Moreover, mutations targeting AIRE-PHD1 affect the formation of a multimeric protein complex at chromatin level. Overall our results reveal the importance of AIRE-PHD domains in the interaction with chromatin-associated nuclear partners and gene regulation confirming the role of PHD fingers as versatile protein interaction hubs for multiple binding events.


  • Organizational Affiliation: 
    • Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milano, Italy.

Macromolecule Content 

  • Total Structure Weight: 6.94 kDa 
  • Atom Count: 473 
  • Modeled Residue Count: 66 
  • Deposited Residue Count: 66 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Autoimmune regulatorA [auth C]66Homo sapiensMutation(s): 0 
Gene Names: AIRE, APECED
UniProt & NIH Common Fund Data Resources
Find proteins for O43918 (Homo sapiens)
Explore O43918 
Go to UniProtKB:  O43918
PHAROS:  O43918
GTEx:  ENSG00000160224 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43918
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth C],
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 50 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2013-01-16
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references