9JGO | pdb_00009jgo

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

• PDB DOI: https://doi.org/10.2210/pdb9JGO/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2024-09-08 Released: 2025-09-10 
• Deposition Author(s): Liu, Y.J., Zhao, M., Chen, C., Hu, X.Y., Kang, H.L., Liu, Q.Q., Huang, X.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.197 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.198 (DCC) 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 21.41 kDa 
• Atom Count: 1,559 
• Modeled Residue Count: 172 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain, N-terminally processed	A	182	Homo sapiens	Mutation(s): 0  Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PD (Subject of Investigation/LOI)	E [auth A], F [auth A]	PALLADIUM ION Pd MUJIDPITZJWBSW-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.197 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.198 (DCC) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.96	α = 90
b = 183.96	β = 90
c = 183.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Liu, Y.J., Zhao, M., Chen, C., Hu, X.Y., Kang, H.L., Liu, Q.Q., Huang, X.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271448
National Natural Science Foundation of China (NSFC)	China	82072054
National Natural Science Foundation of China (NSFC)	China	--
National Natural Science Foundation of China (NSFC)	China	21877065
National Natural Science Foundation of China (NSFC)	China	82111530210

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release