7LVB | pdb_00007lvb

CHOLERA TOXIN B SUBUNIT WITH ATTACHED SIV EPITOPE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 ?
  • R-Value Free: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
View more details

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 1x¦¤V1gp120. 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 ¦¤V1gp120 boost in the SVR yielded more favorable immune responses than its CTB-V2c counterpart. Vaccination with the SVR generates CCR5 - ¦Á4¦Â7 + 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 - ¦Á4¦Â7 + CD4 + T cells and mucosal ¦Á4¦Â7 + 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 ?
  • R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( ? )Angle ( ? )
a = 84.29¦Á = 90
b = 112.428¦Â = 90
c = 137.102¦Ã = 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
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