5LP3 image
Deposition Date 2016-08-11
Release Date 2017-07-26
Last Version Date 2025-04-09
Entry Detail
PDB ID:
5LP3
Keywords:
Title:
Three tetrameric rings of Isoaspartyl Dipeptidase fitted in an EM volume.
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
10.50 Å
Aggregation State:
FILAMENT
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Isoaspartyl dipeptidase
Gene (Uniprot):iadA
Chain IDs:A (auth: B), B (auth: C), C (auth: D), D (auth: E), E (auth: A), F, G, H, I, J, K, L
Chain Length:390
Number of Molecules:12
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
KCX A LYS modified residue
Ligand Molecules
Primary Citation
Proteins evolve on the edge of supramolecular self-assembly.
Nature 548 244 247 (2017)
PMID: 28783726 DOI: 10.1038/nature23320

Abstact

The self-association of proteins into symmetric complexes is ubiquitous in all kingdoms of life. Symmetric complexes possess unique geometric and functional properties, but their internal symmetry can pose a risk. In sickle-cell disease, the symmetry of haemoglobin exacerbates the effect of a mutation, triggering assembly into harmful fibrils. Here we examine the universality of this mechanism and its relation to protein structure geometry. We introduced point mutations solely designed to increase surface hydrophobicity among 12 distinct symmetric complexes from Escherichia coli. Notably, all responded by forming supramolecular assemblies in vitro, as well as in vivo upon heterologous expression in Saccharomyces cerevisiae. Remarkably, in four cases, micrometre-long fibrils formed in vivo in response to a single point mutation. Biophysical measurements and electron microscopy revealed that mutants self-assembled in their folded states and so were not amyloid-like. Structural examination of 73 mutants identified supramolecular assembly hot spots predictable by geometry. A subsequent structural analysis of 7,471 symmetric complexes showed that geometric hot spots were buffered chemically by hydrophilic residues, suggesting a mechanism preventing mis-assembly of these regions. Thus, point mutations can frequently trigger folded proteins to self-assemble into higher-order structures. This potential is counterbalanced by negative selection and can be exploited to design nanomaterials in living cells.

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Primary Citation of related structures