7KE3 | pdb_00007ke3

Heavy chain ferritin with C-terminal EBNA1 epitope


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7KE3

This is version 1.1 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 283.98 kDa 
  • Atom Count: 17,042 
  • Modeled Residue Count: 2,001 
  • Deposited Residue Count: 2,508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferritin heavy chain,Epstein-Barr nuclear antigen 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
209Homo sapiensHuman herpesvirus 4 strain B95-8
This entity is chimeric
Mutation(s): 0 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15EBNA1BKRF1
EC: 1.16.3.1 (PDB Primary Data), 3.1.21 (UniProt)
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
AA [auth F]
EA [auth H]
GA [auth I]
JA [auth K]
M [auth A]
AA [auth F],
EA [auth H],
GA [auth I],
JA [auth K],
M [auth A],
R [auth C]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
FE

Query on FE



Download:Ideal Coordinates CCD File
BA [auth F]
CA [auth G]
DA [auth G]
FA [auth H]
HA [auth I]
BA [auth F],
CA [auth G],
DA [auth G],
FA [auth H],
HA [auth I],
IA [auth J],
KA [auth K],
LA [auth L],
N [auth A],
O [auth A],
P [auth B],
Q [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth D],
W [auth D],
X [auth E],
Y [auth E],
Z [auth E]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.882α = 90
b = 217.882β = 90
c = 147.203γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
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