6JEE

Crystal structure of apo-L161C/L165C-Fr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Coordination design of cadmium ions at the 4-fold axis channel of the apo-ferritin cage.

Abe, S.Ito, N.Maity, B.Lu, C.Lu, D.Ueno, T.

(2019) Dalton Trans 48: 9759-9764

  • DOI: https://doi.org/10.1039/c9dt00609e
  • Primary Citation of Related Structures:  
    6JEE, 6JEF

  • PubMed Abstract: 

    Spherical protein cages with highly symmetrical structures provide unique environments for the conjugation of metal ions and metal nanoparticles. Ferritin has been widely studied as a template for the coordination of metal ions and metal nanoparticles in fundamental research and applications. However, it remains difficult to design metal coordination sites precisely. In this work, we describe the design and construction of new metal coordination sites by introducing Cys residues at the 4-fold symmetrical hydrophobic channel of apo-ferritin. X-ray crystal structure analyses of the mutants containing Cd(ii) ions show that the four or eight binding sites for Cd(ii) ions are located at the 4-fold symmetrical axis channel of apo-ferritin. It was found that the coordination number and configuration of Cd(ii) ions can be varied by adjusting the positions of the Cys residues at the symmetrical channels of the apo-ferritin cage.


  • Organizational Affiliation

    School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan. tueno@bio.titech.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin light chain174Equus caballusMutation(s): 2 
Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus)
Explore P02791 
Go to UniProtKB:  P02791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02791
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.264α = 90
b = 182.264β = 90
c = 182.264γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description