5UP9

Crystal Structure of Zn-bound Human Heavy-Chain ferritin variant 122H-delta C-star with para-xylenedihydroxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Synthetic Modularity of Protein-Metal-Organic Frameworks.

Bailey, J.B.Zhang, L.Chiong, J.A.Ahn, S.Tezcan, F.A.

(2017) J. Am. Chem. Soc. 139: 8160-8166

  • DOI: 10.1021/jacs.7b01202
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Previously, we adopted the construction principles of metal-organic frameworks (MOFs) to design a 3D crystalline protein lattice in which pseudospherical ferritin nodes decorated on their C <sub>3 </sub> symmetric vertices with Zn coordination sites ...

    Previously, we adopted the construction principles of metal-organic frameworks (MOFs) to design a 3D crystalline protein lattice in which pseudospherical ferritin nodes decorated on their C 3 symmetric vertices with Zn coordination sites were connected via a ditopic benzene-dihydroxamate linker. In this work, we have systematically varied both the metal ions presented at the vertices of the ferritin nodes (Zn(II), Ni(II), and Co(II)) and the synthetic dihydroxamate linkers, which yielded an expanded library of 15 ferritin-MOFs with the expected body-centered (cubic or tetragonal) lattice arrangements. Crystallographic and small-angle X-ray scattering (SAXS) analyses indicate that lattice symmetries and dimensions of ferritin-MOFs can be dictated by both the metal and linker components. SAXS measurements on bulk crystalline samples reveal that some ferritin-MOFs can adopt multiple lattice conformations, suggesting dynamic behavior. This work establishes that the self-assembly of ferritin-MOFs is highly robust and that the synthetic modularity that underlies the structural diversity of conventional MOFs can also be applied to the self-assembly of protein-based crystalline materials.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California at San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin heavy chain
A, B, C, D, E, F
182Homo sapiensMutation(s): 5 
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, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BYX
Query on BYX

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Download CCD File 
B
2,2'-(1,4-phenylene)bis(N-hydroxyacetamide)
C10 H12 N2 O4
BKDWYNGFJRBIJD-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A, D
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B, C, D, E, F
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.241 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 149.883α = 90.00
b = 149.883β = 90.00
c = 162.228γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SAINTdata reduction
PHENIXrefinement
SADABSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release