3ERZ

Directing Noble Metal Ion Chemistry within a Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.056 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/bi8016735
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin heavy chain
A, B, C, D, E, F, G, H, I, J, K, L
183Homo sapiensMutation(s): 8 
Gene Names: FTH1 (FTH, FTHL6)
EC: 1.16.3.1
Find proteins for P02794 (Homo sapiens)
Go to Gene View: FTH1
Go to UniProtKB:  P02794
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, G, H, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, G, J
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A, B, C, E, F, G, H, I, K
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
HG
Query on HG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.056 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.199 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 170.941α = 90.00
b = 170.941β = 90.00
c = 190.144γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
ADSCdata collection
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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