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 8DWW | pdb_00008dww

Chikungunya VLP in complex with neutralizing Fab 506.A08 (asymmetric unit)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 543.1 kDa 
  • Atom Count: 37,900 
  • Modeled Residue Count: 4,916 
  • Deposited Residue Count: 4,936 
  • Unique protein chains: 5

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E1 glycoproteinA [auth B],
F [auth A],
K [auth C],
P [auth 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
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
506.A08 heavy chainB [auth H],
G [auth V],
L [auth X],
Q [auth Z]		119Homo sapiensMutation(s): 0 
Entity Groups
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
506.A08 light chainC [auth L],
H [auth U],
M [auth W],
R [auth Y]		106Homo sapiensMutation(s): 0 
Entity Groups
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
E2 glycoproteinD [auth N],
I [auth M],
N [auth O],
S [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
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Reference Sequence
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid proteinE [auth R],
J [auth Q],
O [auth S],
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
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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 C]
BA [auth O]
CA [auth O]
DA [auth D]
EA [auth P]
AA [auth C],
BA [auth O],
CA [auth O],
DA [auth D],
EA [auth P],
FA [auth P],
U [auth B],
V [auth N],
W [auth N],
X [auth A],
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: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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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: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-05-28
    Changes: Data collection