5U1A

Ferritin with Gc MtrE loop 1 inserted at His34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-based design of ferritin nanoparticle immunogens displaying antigenic loops of Neisseria gonorrhoeae.

Wang, L.Xing, D.Le Van, A.Jerse, A.E.Wang, S.

(2017) FEBS Open Bio 7: 1196-1207

  • DOI: https://doi.org/10.1002/2211-5463.12267
  • Primary Citation of Related Structures:  
    5U1A, 5U1B

  • PubMed Abstract: 

    Effective vaccines are urgently needed to combat gonorrhea, a common sexually transmitted bacterial infection, for which treatment options are diminishing due to rapid emergence of antibiotic resistance. We have used a rational approach to the development of gonorrhea vaccines, and genetically engineered nanoparticles to present antigenic peptides of Neisseria gonorrhoeae , the causative agent of gonorrhea. We hypothesized that the ferritin nanocage could be used as a platform to display an ordered array of N. gonorrhoeae antigenic peptides on its surface. MtrE, the outer membrane channel of the highly conserved gonococcal MtrCDE active efflux pump, is an attractive vaccine target due to its importance in protecting N. gonorrhoeae from host innate effectors and antibiotic resistance. Using computational approaches, we designed constructs that expressed chimeric proteins of the Helicobacter pylori ferritin and antigenic peptides that correspond to the two surface-exposed loops of N. gonorrhoeae MtrE. The peptides were inserted at the N terminus or in a surface-exposed ferritin loop between helices αA and αB. Crystal structures of the chimeric proteins revealed that the proteins assembled correctly into a 24-mer nanocage structure. Although the inserted N. gonorrhoeae peptides were disordered, it was clear that they were displayed on the nanocage surface, but with multiple conformations. Our results confirmed that the ferritin nanoparticle is a robust platform to present antigenic peptides and therefore an ideal system for rational design of immunogens.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology Uniformed Services University of the Health Sciences Bethesda MD USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin,MtrE protein chimera
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
182Helicobacter pyloriNeisseria gonorrhoeaeMutation(s): 0 
Gene Names: AM498_04815HPY173_00920HPY207_01135OA23_03490mtrE
EC: 1.16.3.2
UniProt
Find proteins for Q51006 (Neisseria gonorrhoeae)
Explore Q51006 
Go to UniProtKB:  Q51006
Find proteins for P52093 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P52093 
Go to UniProtKB:  P52093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ51006P52093
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth I]
EA [auth F]
KA [auth F]
LA [auth F]
MB [auth L]
AB [auth I],
EA [auth F],
KA [auth F],
LA [auth F],
MB [auth L],
R [auth B],
T [auth C],
U [auth C],
VA [auth H],
X [auth D],
Y [auth D],
ZA [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
DA [auth E]
EB [auth K]
JA [auth F]
LB [auth L]
O [auth A]
DA [auth E],
EB [auth K],
JA [auth F],
LB [auth L],
O [auth A],
PA [auth G]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
FB [auth K]
MA [auth F]
NB [auth L]
OB [auth L]
PB [auth L]
FB [auth K],
MA [auth F],
NB [auth L],
OB [auth L],
PB [auth L],
QA [auth G],
V [auth C],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
BB [auth J]
CA [auth E]
CB [auth K]
AA [auth E],
BA [auth E],
BB [auth J],
CA [auth E],
CB [auth K],
DB [auth K],
FA [auth F],
GA [auth F],
GB [auth L],
HA [auth F],
HB [auth L],
IA [auth F],
IB [auth L],
JB [auth L],
KB [auth L],
M [auth A],
N [auth A],
NA [auth G],
OA [auth G],
P [auth B],
Q [auth B],
RA [auth G],
S [auth C],
SA [auth H],
TA [auth H],
UA [auth H],
W [auth D],
WA [auth H],
XA [auth I],
YA [auth I]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.412α = 90
b = 128.412β = 90
c = 165.041γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
HKLdata scaling
HKLdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2017-10-11 
  • Deposition Author(s): Wang, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description