7LVB

CHOLERA TOXIN B SUBUNIT WITH ATTACHED SIV EPITOPE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Cholera toxin B scaffolded, focused SIV V2 epitope elicits antibodies that influence the risk of SIV mac251 acquisition in macaques.

Rahman, M.A.Becerra-Flores, M.Patskovsky, Y.Silva de Castro, I.Bissa, M.Basu, S.Shen, X.Williams, L.D.Sarkis, S.N'guessan, K.F.LaBranche, C.Tomaras, G.D.Aye, P.P.Veazey, R.Paquin-Proulx, D.Rao, M.Franchini, G.Cardozo, T.

(2023) Front Immunol 14: 1139402-1139402

  • DOI: https://doi.org/10.3389/fimmu.2023.1139402
  • Primary Citation of Related Structures:  
    7LVB

  • PubMed Abstract: 

    An efficacious HIV vaccine will need to elicit a complex package of innate, humoral, and cellular immune responses. This complex package of responses to vaccine candidates has been studied and yielded important results, yet it has been a recurring challenge to determine the magnitude and protective effect of specific in vivo immune responses in isolation. We therefore designed a single, viral-spike-apical, epitope-focused V2 loop immunogen to reveal individual vaccine-elicited immune factors that contribute to protection against HIV/SIV. We generated a novel vaccine by incorporating the V2 loop B-cell epitope in the cholera toxin B (CTB) scaffold and compared two new immunization regimens to a historically protective 'standard' vaccine regimen (SVR) consisting of 2xDNA prime boosted with 2xALVAC-SIV and 1xΔV1gp120. We immunized a cohort of macaques with 5xCTB-V2c vaccine+alum intramuscularly simultaneously with topical intrarectal vaccination of CTB-V2c vaccine without alum (5xCTB-V2/alum). In a second group, we tested a modified version of the SVR consisting of 2xDNA prime and boosted with 1xALVAC-SIV and 2xALVAC-SIV+CTB-V2/alum, (DA/CTB-V2c/alum). In the absence of any other anti-viral antibodies, V2c epitope was highly immunogenic when incorporated in the CTB scaffold and generated highly functional anti-V2c antibodies in the vaccinated animals. 5xCTB-V2c/alum vaccination mediated non-neutralizing ADCC activity and efferocytosis, but produced low avidity, trogocytosis, and no neutralization of tier 1 virus. Furthermore, DA/CTB-V2c/alum vaccination also generated lower total ADCC activity, avidity, and neutralization compared to the SVR. These data suggest that the ΔV1gp120 boost in the SVR yielded more favorable immune responses than its CTB-V2c counterpart. Vaccination with the SVR generates CCR5 - α4β7 + CD4 + Th1, Th2, and Th17 cells, which are less likely to be infected by SIV/HIV and likely contributed to the protection afforded in this regimen. The 5xCTB-V2c/alum regimen likewise elicited higher circulating CCR5 - α4β7 + CD4 + T cells and mucosal α4β7 + CD4 + T cells compared to the DA/CTB-V2c/alum regimen, whereas the first cell type was associated with reduced risk of viral acquisition. Taken together, these data suggest that individual viral spike B-cell epitopes can be highly immunogenic and functional as isolated immunogens, although they might not be sufficient on their own to provide full protection against HIV/SIV infection.


  • Organizational Affiliation

    Animal Models and Retroviral Vaccines Section, National Cancer Institute, NIH Bethesda, MD, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholera enterotoxin B-subunit,Surface protein gp120117Vibrio choleraeSimian immunodeficiency virus
This entity is chimeric
Mutation(s): 1 
Gene Names: ctxBC9J66_18955ERS013165_03981ERS013197_06217ERS013202_03762ERS013206_03003env
UniProt
Find proteins for P19503 (Simian immunodeficiency virus (isolate PBj14/BCL-3))
Explore P19503 
Go to UniProtKB:  P19503
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01556 
Go to UniProtKB:  P01556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP19503P01556
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download Ideal Coordinates CCD File 
AA [auth A]
EA [auth B]
JA [auth C]
K [auth D]
NA [auth I]
AA [auth A],
EA [auth B],
JA [auth C],
K [auth D],
NA [auth I],
O [auth E],
R [auth F],
RA [auth J],
U [auth G],
Y [auth H]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
BA [auth A]
CA [auth A]
FA [auth B]
GA [auth B]
KA [auth C]
BA [auth A],
CA [auth A],
FA [auth B],
GA [auth B],
KA [auth C],
L [auth D],
LA [auth C],
M [auth D],
OA [auth I],
P [auth E],
PA [auth I],
S [auth F],
SA [auth J],
T [auth F],
V [auth G]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth A]
HA [auth B]
IA [auth B]
MA [auth C]
N [auth D]
DA [auth A],
HA [auth B],
IA [auth B],
MA [auth C],
N [auth D],
Q [auth E],
QA [auth I],
TA [auth J],
W [auth G],
X [auth G],
Z [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.29α = 90
b = 112.428β = 90
c = 137.102γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States272201300004I-P00005-27200007-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-10-18
    Changes: Refinement description