6MB2

Cryo-EM structure of the PYD filament of AIM2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Plasticity in PYD assembly revealed by cryo-EM structure of the PYD filament of AIM2.

Lu, A.Li, Y.Yin, Q.Ruan, J.Yu, X.Egelman, E.Wu, H.

(2015) Cell Discov 1: --

  • DOI: 10.1038/celldisc.2015.13

  • PubMed Abstract: 
  • Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1 to form the AIM2 inflammasome, wh ...

    Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1 to form the AIM2 inflammasome, which leads to proteolytic maturation of cytokines and pyroptotic cell death. AIM2 contains an N-terminal Pyrin domain (PYD) that interacts with ASC through PYD/PYD interactions and nucleates ASC PYD filament formation. To elucidate the molecular basis of AIM2-induced ASC PYD polymerization, we generated AIM2 PYD filaments fused to green fluorescent protein (GFP) and determined its cryo-electron microscopic (cryo-EM) structure. The map showed distinct definition of helices, allowing fitting of the crystal structure. Surprisingly, the GFP-AIM2 PYD filament is a 1-start helix with helical parameters distinct from those of the 3-start ASC PYD filament. However, despite the apparent symmetry difference, helical net and detailed interface analyses reveal minimal changes in subunit packing. GFP-AIM2 PYD nucleated ASC PYD filament formation in comparable efficiency as untagged AIM2 PYD , suggesting assembly plasticity in both AIM2 PYD and ASC PYD . The DNA-binding domain of AIM2 is able to form AIM2/DNA filaments, within which the AIM2 PYD is brought into proximity to template ASC PYD filament assembly. Because ASC is able to interact with many PYD-containing receptors for the formation of inflammasomes, the observed structural plasticity may be critically important for this versatility in the PYD/PYD interactions.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA ; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interferon-inducible protein AIM2
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
94Homo sapiensMutation(s): 0 
Gene Names: AIM2
Find proteins for O14862 (Homo sapiens)
Go to Gene View: AIM2
Go to UniProtKB:  O14862
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
a, b, c, d, e, f, g, h, i, j, k, l, m, n, o
228Aequorea victoriaMutation(s): 0 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
a, b, c, d, e, f, g, h, i, j, k, l, m, n, o
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
CRO
Query on CRO
a, b, c, d, e, f, g, h, i, j, k, l, m, n, o
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-08-29 
  • Released Date: 2018-09-05 
  • Deposition Author(s): Lu, A., Li, Y., Wu, H.

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release