5GN8

Structure of a 48-mer protein nanocage fabricated from its 24-mer analogue by subunit interface redesign


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.805 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

"Silent" Amino Acid Residues at Key Subunit Interfaces Regulate the Geometry of Protein Nanocages

Zhang, S.Zang, J.Zhang, X.Chen, H.Mikami, B.Zhao, G.

(2016) ACS Nano 10: 10382-10388

  • DOI: 10.1021/acsnano.6b06235

  • PubMed Abstract: 
  • Rendering the geometry of protein-based assemblies controllable remains challenging. Protein shell-like nanocages represent particularly interesting targets for designed assembly. Here, we introduce an engineering strategy-key subunit interface redes ...

    Rendering the geometry of protein-based assemblies controllable remains challenging. Protein shell-like nanocages represent particularly interesting targets for designed assembly. Here, we introduce an engineering strategy-key subunit interface redesign (KSIR)-that alters a natural subunit-subunit interface by selective deletion of a small number of "silent" amino acid residues (no participation in interfacial interactions) into one that triggers the generation of a non-native protein cage. We have applied KSIR to construct a non-native 48-mer nanocage from its native 24-mer recombinant human H-chain ferritin (rHuHF). This protein is a heteropolymer composed of equal numbers of two different subunits which are derived from one polypeptide. This strategy has allowed the study of conversion between protein nanocages with different geometries by re-engineering key subunit interfaces and the demonstration of the important role of the above-mentioned specific residues in providing geometric specificity for protein assembly.


    Organizational Affiliation

    Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University , Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin heavy chain
A
176Homo sapiensMutation(s): 0 
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ferritin heavy chain
B
146Homo sapiensMutation(s): 0 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.805 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 236.120α = 90.00
b = 236.120β = 90.00
c = 236.120γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China--

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2019-07-24
    Type: Data collection, Derived calculations