8DEQ

Cryo-EM local refinement of antibody SKV09 in complex with VEEV alphavirus spike glycoprotein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 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

Vaccine elicitation and structural basis for antibody protection against alphaviruses.

Sutton, M.S.Pletnev, S.Callahan, V.Ko, S.Tsybovsky, Y.Bylund, T.Casner, R.G.Cerutti, G.Gardner, C.L.Guirguis, V.Verardi, R.Zhang, B.Ambrozak, D.Beddall, M.Lei, H.Yang, E.S.Liu, T.Henry, A.R.Rawi, R.Schon, A.Schramm, C.A.Shen, C.H.Shi, W.Stephens, T.Yang, Y.Florez, M.B.Ledgerwood, J.E.Burke, C.W.Shapiro, L.Fox, J.M.Kwong, P.D.Roederer, M.

(2023) Cell 186: 2672-2689.e25

  • DOI: https://doi.org/10.1016/j.cell.2023.05.019
  • Primary Citation of Related Structures:  
    8DEC, 8DED, 8DEE, 8DEF, 8DEQ, 8DER, 8DUL, 8DUN, 8DWO, 8EEU, 8EEV

  • PubMed Abstract: 

    Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine encephalitis virus-like particles (VLPs), a regimen that protects against aerosol challenge with all three viruses. Single- and triple-virus-specific antibodies were isolated, and we identified 21 unique binding groups. Cryo-EM structures revealed that broad VLP binding inversely correlated with sequence and conformational variability. One triple-specific antibody, SKT05, bound proximal to the fusion peptide and neutralized all three Env-pseudotyped encephalitic alphaviruses by using different symmetry elements for recognition across VLPs. Neutralization in other assays (e.g., chimeric Sindbis virus) yielded variable results. SKT05 bound backbone atoms of sequence-diverse residues, enabling broad recognition despite sequence variability; accordingly, SKT05 protected mice against Venezuelan equine encephalitis virus, chikungunya virus, and Ross River virus challenges. Thus, a single vaccine-elicited antibody can protect in vivo against a broad range of alphaviruses.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E1
A, B, C, D, E
A, B, C, D, E, F
402Venezuelan equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for P05674 (Venezuelan equine encephalitis virus (strain TC-83))
Explore P05674 
Go to UniProtKB:  P05674
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05674
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SKV09 Fab Heavy ChainG [auth H]120MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SKV09 Fab Light ChainH [auth L]107MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary