Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 21.99 kDa 
• Atom Count: 1460 
• Residue Count: 172 
• Unique protein chains: 1

3ES3

Directing Noble Metal Ion Chemistry within a Designed Ferritin Protein. The Complex with Gold ions. Ferritin H8-H9x Mutant

• DOI: 10.2210/pdb3ES3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-03 Released: 2008-10-21 
• Deposition Author(s): Di Costanzo, L., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.275 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Literature

Directing noble metal ion chemistry within a designed ferritin protein.

Butts, C.A., Swift, J., Kang, S.G., Di Costanzo, L., Christianson, D.W., Saven, J.G., Dmochowski, I.J.

(2008) Biochemistry 47: 12729-12739

• PubMed: 18991401 
• DOI: 10.1021/bi8016735
• Primary Citation of Related Structures:  
  3ERZ, 3ES3, 2Z6M


• PubMed Abstract: 
  

Human H ferritin (HuHF) assembles from 24 four-helix bundles to form an approximately 500 kDa protein with an 8 nm internal cavity. HuHF provides a useful model for studying the transport of metal ions in solution to buried reaction sites in proteins. In this study, HuHF was redesigned to facilitate noble metal ion (Au(3+), Ag(+)) binding, reduction, and nanoparticle formation within the cavity. Computationally determined amino acid substitutions were targeted at four external and four internal surface sites. A variant with a total of 96 cysteines and histidines removed from the exterior surface and 96 non-native cysteines added to the interior surface retained wild-type stability and structure, as confirmed by X-ray crystallography, and promoted the formation of silver or gold nanoparticles within the protein cavity. Crystallographic studies with HuHF variants provide insight into how ferritins control access of metal ions to interior residues that perform chemistry.

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Organizational Affiliation: 

Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	A	183	Homo sapiens	Mutation(s): 10  Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 EC: 1.16.3.1
Find proteins for P02794 (Homo sapiens) Explore P02794  Go to UniProtKB:  P02794
NIH Common Fund Data Resources
PHAROS  P02794 GTEx  ENSG00000167996

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	A	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.275 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.564	α = 90
b = 181.564	β = 90
c = 181.564	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-03 
• Released Date: 2008-10-21 
Deposition Author(s): Di Costanzo, L., Christianson, D.W.

Revision History 

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description