9AZI image
Deposition Date 2024-03-11
Release Date 2024-05-01
Last Version Date 2025-08-13
Entry Detail
PDB ID:
9AZI
Keywords:
Title:
NMR solution structure of cell-permeant miniature protein ZF5.3
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Conformers Calculated:
200
Conformers Submitted:
20
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Designed Zinc finger protein 5.3
Gene (Uniprot):ZNF473
Chain IDs:A
Chain Length:27
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
The biophysical requirements that govern the efficient endosomal escape of designed mini-proteins.
Nat.Chem. 17 1227 1235 (2025)
PMID: 40629095 DOI: 10.1038/s41557-025-01846-4

Abstact

The ZF5.3 mini-protein escapes endosomes efficiently to guide proteins into the cytosol and/or nucleus. However, other than the requirement for small or unfoldable cargo and an intact HOPS complex, little is known about how ZF5.3 traverses the limiting endocytic membrane. Here we characterize the requirements for efficient endosomal escape. We confirm that ZF5.3 remains folded at high temperatures and at pH values between 5.5 and 7.5. At lower pH, ZF5.3 unfolds cooperatively upon protonation of Zn(II)-binding His side chains whose pKa matches that of the late endolysosomal lumen. pH-induced unfolding of ZF5.3 is essential for endosomal escape, as an analogue that remains folded at low pH fails to efficiently reach the cytosol. Once unfolded, ZF5.3 interacts in a pH-dependent manner with bis(monoacylglycero)phosphate, a lipid present in the inner leaflet of late endolysosomal membranes. These data provide a biophysical model for HOPS-dependent endosomal escape.

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Primary Citation of related structures