3ERZ | pdb_00003erz

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: 3.06 Å
  • R-Value Free: 
    0.256 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3ERZ

This is version 1.4 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: https://doi.org/10.1021/bi8016735
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 257.84 kDa 
  • Atom Count: 17,139 
  • Modeled Residue Count: 2,064 
  • Deposited Residue Count: 2,196 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
183Homo sapiensMutation(s): 8 
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HG

Query on HG



Download:Ideal Coordinates CCD File
AA [auth F]
CA [auth G]
HA [auth H]
KA [auth I]
MA [auth J]
AA [auth F],
CA [auth G],
HA [auth H],
KA [auth I],
MA [auth J],
N [auth A],
PA [auth K],
QA [auth L],
S [auth B],
V [auth C],
W [auth D],
Y [auth E]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
BA [auth G]
FA [auth H]
GA [auth H]
JA [auth I]
M [auth A]
BA [auth G],
FA [auth H],
GA [auth H],
JA [auth I],
M [auth A],
OA [auth K],
Q [auth B],
R [auth B],
U [auth C],
X [auth E],
Z [auth F]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
EA [auth G],
IA [auth H],
LA [auth I],
P [auth A],
T [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
DA [auth G],
NA [auth J],
O [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free:  0.256 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.941α = 90
b = 170.941β = 90
c = 190.144γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection