› 8der

Electron Microscopy
3.3Å resolution

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

Released:
DOI: 10.2210/pdb8der/pdb
PDB entry 8der coloured by chain, front view.
PDB entry 8der coloured by chain, side view.
PDB entry 8der coloured by chain, top view.
Source organisms:
Primary publication:
Vaccine elicitation and structural basis for antibody protection against alphaviruses.
Sutton MS, Pletnev S, Callahan V, Ko S, Tsybovsky Y, Bylund T, Casner RG, Cerutti G, Gardner CL, Guirguis V, Verardi R, Zhang B, Ambrozak D, Beddall M, Lei H, Yang ES, Liu T, Henry AR, Rawi R, Schön A, Schramm CA, Shen CH, Shi W, Stephens T, Yang Y, Florez MB, Ledgerwood JE, Burke CW, Shapiro L, Fox JM, Kwong PD, Roederer M
Cell 186 2672-2689.e25 (2023)
PMID: 37295404
Related structures: EMD-27396

Function and Biology Details

Reaction catalysed: 
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
Biochemical function:
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-225071 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
SKV16 Fab Heavy Chain Chains: H, W, X
Molecule details ›
Chains: H, W, X
Length: 122 amino acids
Theoretical weight: 13.46 KDa
Source organism: Macaca
Expression system: Homo sapiens
SKV16 Fab Light Chain Chains: L, V, Y
Molecule details ›
Chains: L, V, Y
Length: 105 amino acids
Theoretical weight: 11.21 KDa
Source organism: Macaca
Expression system: Homo sapiens
Spike glycoprotein E1 Chains: E, F, G
Molecule details ›
Chains: E, F, G
Length: 402 amino acids
Theoretical weight: 43.67 KDa
Source organism: Venezuelan equine encephalitis virus
Expression system: Homo sapiens
UniProt:
  • Canonical: P05674 (Residues: 813-1214; Coverage: 32%)
Sequence domains: Alphavirus E1 glycoprotein
Spike glycoprotein E2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 345 amino acids
Theoretical weight: 38.57 KDa
Source organism: Venezuelan equine encephalitis virus
Expression system: Homo sapiens
UniProt:
  • Canonical: P05674 (Residues: 335-679; Coverage: 28%)
Sequence domains: Alphavirus E2 glycoprotein

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-27396
Expression system: Homo sapiens

Quick links

Citations

1 citations in other articles

Antibody offers broad alphavirus protection.
Crunkhorn S. (2023)