6KH5

Design and crystal structure of protein MOFs with ferritin nanocages as linkers and nickel clusters as nodes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.163 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Insight into Binary Protein Metal-Organic Frameworks with Ferritin Nanocages as Linkers and Nickel Clusters as Nodes.

Gu, C.Chen, H.Wang, Y.Zhang, T.Wang, H.Zhao, G.

(2020) Chemistry 26: 3016-3021

  • DOI: https://doi.org/10.1002/chem.201905315
  • Primary Citation of Related Structures:  
    6KH0, 6KH1, 6KH3, 6KH4, 6KH5

  • PubMed Abstract: 

    Metal-organic frameworks (MOFs) hold great promise for numerous applications. However, proteins, carriers of biological functions in living systems, have not yet been fully explored as building blocks for the construction of MOFs. This work presents a strategy for the fabrication of binary MOFs. Considering octahedral ferritin symmetry, four His 2 (His-His) motifs were first incorporated into the exterior surface of a ferritin nanocage near each C 4 channel, yielding protein linkers with multiple metal-binding sites (bisH-SF). Secondly, by adding nickel ions to bisH-SF solutions triggers the self-assembly of ferritin nanocages into a porous 3D crystalline MOF with designed protein lattice, where two adjacent ferritin molecules along the C 4 symmetry axes are bridged by four dinuclear or tetranuclear nickel clusters depending on Ni 2+ concentration. This work provides a simple approach for precise control over a binary protein-metal crystalline framework, and the resulting MOFs exhibited inherent ferroxidase activity and peroxidase-like catalytic activity.


  • Organizational Affiliation

    Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin170Penaeus japonicusMutation(s): 1 
EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus)
Explore T2B7E1 
Go to UniProtKB:  T2B7E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2B7E1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.163 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.533α = 90
b = 118.533β = 90
c = 118.533γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31730069
National Natural Science Foundation of China (NSFC)China31671805

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description