8DER | pdb_00008der

Cryo-EM local refinement of antibody SKV16 in complex with VEEV alphavirus spike glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb8DER/pdb
• EM Map EMD-27396: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Macaca, Venezuelan equine encephalitis virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-06-21 Released: 2023-06-28 
• Deposition Author(s): Casner, R.G., Verardi, R., Roederer, M., Shapiro, L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 37295404 
• DOI: https://doi.org/10.1016/j.cell.2023.05.019
• Primary Citation 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.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA.
Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA. Electronic address: [e-mail].
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 322.86 kDa 
• Atom Count: 22,665 
• Modeled Residue Count: 2,921 
• Deposited Residue Count: 2,922 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SKV16 Fab Heavy Chain	A [auth X], I [auth H], K [auth W]	122	Macaca	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SKV16 Fab Light Chain	B [auth Y], J [auth L], L [auth V]	105	Macaca	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E1	C [auth G], D [auth E], F	402	Venezuelan equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for P05674 (Venezuelan equine encephalitis virus (strain TC-83)) Explore P05674  Go to UniProtKB:  P05674
Glycosylation
Glycosylation Sites: 1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E2	E [auth C], G [auth B], H [auth A]	345	Venezuelan equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for P05674 (Venezuelan equine encephalitis virus (strain TC-83)) Explore P05674  Go to UniProtKB:  P05674
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth D], N [auth I]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O [auth J]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth G], Q [auth E], R [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Casner, R.G., Verardi, R., Roederer, M., Shapiro, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.2: 2025-05-14
  Changes: Data collection