9JGP | pdb_00009jgp

Structure of Pd ions bound to human heavy chain ferritin nanocage.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.184 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Granzyme B-mimetic nanozyme for nanovesicle targeted anticancer applications.

Hu, X.Liu, Q.Kang, H.Zhao, M.Zhou, Z.Li, Y.Peng, W.Qi, T.Liu, R.Jiao, L.Zhuang, J.Liu, Y.Mann, S.Huang, X.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-68773-x
  • Primary Citation Related Structures: 
    9JGO, 9JGP

  • PubMed Abstract: 

    Cytotoxic T lymphocytes play a crucial role in anti-tumour immunity, with granzyme B (GrB) being a decisive factor in this process. Developing a GrB-based delivery system to mimic T cell-based immunotherapy holds promise but remains challenging. Here, we present an artificial metalloenzyme (nanozyme) with GrB-like protease activity capable of inducing caspase-dependent cell apoptosis. The nanozyme is based on the site-specific binding of Pd(II) ions to recombinant human heavy chain apo-ferritin nanocages to generate a binuclear catalytic centre consisting of two Pd atoms with bridging cysteine ligands, monodentate methionine and histidine residues, and two water molecules. We show that encapsulation of the Pd-ferritin complex within membrane-fused lipid nanoparticles comprising surface-displayed single-chain antibodies affords GrB-mimicking nanozyme-based nanovesicles capable of receptor-mediated delivery of the nanozyme into the cytoplasm of tumour cells and induction of caspase-dependent apoptosis. This study provides valuable insights into the construction of nano-delivery systems with artificial GrB activity and presents a promising therapeutic option for solid tumours.


  • Organizational Affiliation
    • Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers Science Centre for Cell Responses, Nankai University, Tianjin, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin heavy chain, N-terminally processed182Homo sapiensMutation(s): 5 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
PHAROS:  P02794
GTEx:  ENSG00000167996 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02794
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PD
Query on PD

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
PALLADIUM ION
Pd
MUJIDPITZJWBSW-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.184 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.7α = 90
b = 183.7β = 90
c = 183.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32271448
National Natural Science Foundation of China (NSFC)China82072054
National Natural Science Foundation of China (NSFC)China21877065
National Natural Science Foundation of China (NSFC)China82111530210

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references