8DWX

Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A chikungunya virus-like particle vaccine induces broadly neutralizing and protective antibodies against alphaviruses in humans.

Raju, S.Adams, L.J.Earnest, J.T.Warfield, K.Vang, L.Crowe Jr., J.E.Fremont, D.H.Diamond, M.S.

(2023) Sci Transl Med 15: eade8273-eade8273

  • DOI: https://doi.org/10.1126/scitranslmed.ade8273
  • Primary Citation of Related Structures:  
    8DWW, 8DWX, 8DWY

  • PubMed Abstract: 

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes epidemics of acute and chronic musculoskeletal disease. Here, we analyzed the human B cell response to a CHIKV-like particle-adjuvanted vaccine (PXVX0317) from samples obtained from a phase 2 clinical trial in humans (NCT03483961). Immunization with PXVX0317 induced high levels of neutralizing antibody in serum against CHIKV and circulating antigen-specific B cells up to 6 months after immunization. Monoclonal antibodies (mAbs) generated from peripheral blood B cells of three PXVX0317-vaccinated individuals on day 57 after immunization potently neutralized CHIKV infection, and a subset of these inhibited multiple related arthritogenic alphaviruses. Epitope mapping and cryo-electron microscopy defined two broadly neutralizing mAbs that uniquely bind to the apex of the B domain of the E2 glycoprotein. These results demonstrate the inhibitory breadth and activity of the human B cell response induced by the PXVX0317 vaccine against CHIKV and potentially other related alphaviruses.


  • Organizational Affiliation

    Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E1 glycoprotein
A, B, C, D
439Chikungunya virus strain Senegal 37997Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XXP3
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E2 glycoproteinE [auth M],
F [auth N],
G [auth O],
H [auth P]
419Chikungunya virus strain Senegal 37997Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XXP3
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid proteinI [auth Q],
J [auth R],
K [auth S],
L [auth T]
151Chikungunya virus strain Senegal 37997Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XXP3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
506.C01 light chainM [auth L],
P [auth U],
R [auth W],
T [auth Y]
107Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
506.C01 heavy chainN [auth H],
O [auth V],
Q [auth X],
S [auth Z]
128Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth N]
BA [auth N]
CA [auth O]
DA [auth O]
EA [auth P]
AA [auth N],
BA [auth N],
CA [auth O],
DA [auth O],
EA [auth P],
FA [auth P],
U [auth A],
V [auth B],
W [auth C],
X [auth D],
Y [auth M],
Z [auth M]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93019C00062
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary