Crystal structure of Human Ferritin H8 as biotemplate for noble metal nanoparticle synthesis

Experimental Data Snapshot

  • Resolution: 2.72 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/bi8016735
  • Primary Citation of Related Structures:  
    2Z6M, 3ERZ, 3ES3

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin heavy chain
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
176Homo sapiensMutation(s): 8 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
PHAROS:  P02794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02794
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth L]
Q [auth B]
R [auth C]
S [auth E]
AA [auth I],
BA [auth L],
Q [auth B],
R [auth C],
S [auth E],
T [auth F],
Y [auth H]
C6 H14 O2
Query on ZN

Download Ideal Coordinates CCD File 
M [auth A],
O [auth B],
U [auth G],
W [auth H],
Z [auth I]
Query on CA

Download Ideal Coordinates CCD File 
N [auth A],
P [auth B],
V [auth G],
X [auth H]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.72 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.294α = 90
b = 171.294β = 90
c = 190.455γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description