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: 2.81 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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
  • Primary Citation of Related Structures:  
    5GN8

  • 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 redesign ...

    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: 

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferritin heavy chain A176Homo sapiensMutation(s): 0 
Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15
EC: 1.16.3.1
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
NIH Common Fund Data Resources
PHAROS:  P02794
GTEx:  ENSG00000167996
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ferritin heavy chain B146Homo sapiensMutation(s): 0 
Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15
EC: 1.16.3.1
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
NIH Common Fund Data Resources
PHAROS:  P02794
GTEx:  ENSG00000167996
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 236.12α = 90
b = 236.12β = 90
c = 236.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling

Structure Validation

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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
    Changes: Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Derived calculations