Heavy chain ferritin with N-terminal EBNA1 epitope

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Immunogenicity study of engineered ferritins with C- and N-terminus insertion of Epstein-Barr nuclear antigen 1 epitope.

Qu, Y.Zhang, B.Wang, Y.Yin, S.Pederick, J.L.Bruning, J.B.Sun, Y.Middelberg, A.Bi, J.

(2021) Vaccine 39: 4830-4841

  • DOI: https://doi.org/10.1016/j.vaccine.2021.07.021
  • Primary Citation of Related Structures:  
    7KE3, 7KE5

  • PubMed Abstract: 

    Human ferritin heavy chain, an example of a protein nanoparticle, has recently been used as a vaccine delivery platform. Human ferritin has advantages of uniform architecture, robust thermal and chemical stabilities, and good biocompatibility and biodegradation. There is however a lack of understanding about the relationship between insertion sites in ferritin (N-terminus and C-terminus) and the corresponding humoral and cell-mediated immune responses. To bridge this gap, we utilized an Epstein-Barr Nuclear Antigen 1 (EBNA1) epitope as a model to produce engineered ferritin-based vaccines E1F1 (N-terminus insertion) and F1E1 (C-terminus insertion) for the prevention of Epstein-Barr virus (EBV) infections. X-ray crystallography confirmed the relative positions of the N-terminus insertion and C-terminus insertion. For N-terminus insertion, the epitopes were located on the exterior surface of ferritin, while for C-terminus insertion, the epitopes were inside the ferritin cage. Based on the results of antigen-specific antibody titers from in-vivo tests, we found that there was no obvious difference on humoral immune responses between N-terminus and C-terminus insertion. We also evaluated splenocyte proliferation and memory lymphocyte T cell differentiation. Both results suggested C-terminus insertion produced a stronger proliferative response and cell-mediated immune response than N-terminus insertion. C-terminus insertion of EBNA1 epitope was also processed more efficiently by dendritic cells (DCs) than N-terminus insertion. This provides new insight into the relationship between the insertion site and immunogenicity of ferritin nanoparticle vaccines.

  • Organizational Affiliation

    School of Chemical Engineering and Advanced Materials, Faculty of Engineering, Computer and Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epstein-Barr nuclear antigen 1,Ferritin heavy chain
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
209Human herpesvirus 4 strain B95-8Homo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
PHAROS:  P02794
GTEx:  ENSG00000167996 
Find proteins for P03211 (Epstein-Barr virus (strain B95-8))
Explore P03211 
Go to UniProtKB:  P03211
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP03211P02794
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TRS

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
GA [auth L]
M [auth A]
Q [auth C]
AA [auth H],
CA [auth I],
GA [auth L],
M [auth A],
Q [auth C],
V [auth E]
C4 H12 N O3
Query on FE

Download Ideal Coordinates CCD File 
BA [auth H]
DA [auth I]
EA [auth J]
FA [auth K]
HA [auth L]
BA [auth H],
DA [auth I],
EA [auth J],
FA [auth K],
HA [auth L],
N [auth A],
O [auth A],
P [auth B],
R [auth C],
S [auth C],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Y [auth F],
Z [auth G]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.277 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.323α = 90
b = 219.323β = 90
c = 148.556γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description