9AZI | pdb_00009azi

NMR solution structure of cell-permeant miniature protein ZF5.3


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The biophysical requirements that govern the efficient endosomal escape of designed mini-proteins.

Giudice, J.Brauer, D.D.Zoltek, M.Vazquez-Maldonado, A.L.Dadina, N.Kelly, M.Schepartz, A.

(2025) Nat Chem 17: 1227-1235

  • DOI: https://doi.org/10.1038/s41557-025-01846-4
  • Primary Citation of Related Structures:  
    9AZI

  • PubMed Abstract: 

    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 pK a 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.


  • Organizational Affiliation
    • Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Designed Zinc finger protein 5.327Homo sapiensMutation(s): 0 
Gene Names: ZNF473KIAA1141ZFP100
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTR7 (Homo sapiens)
Explore Q8WTR7 
Go to UniProtKB:  Q8WTR7
PHAROS:  Q8WTR7
GTEx:  ENSG00000142528 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WTR7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2203903
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134963

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Database references, Structure summary
  • Version 1.2: 2025-08-13
    Changes: Database references