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

Electron Microscopy
6Å resolution
PDB entry 8deq coloured by chain, front view.
PDB entry 8deq coloured by chain, side view.
PDB entry 8deq coloured by chain, top view.
Source organisms:
Assembly composition:
hetero octamer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Capsid protein and IG-heavy chain and IG-light kappa chain
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Multimeric state: hetero octamer
Accessible surface area: 122005.72 Å2
Buried surface area: 4540.16 Å2
Dissociation area: 1,617.63 Å2
Dissociation energy (ΔGdiss): -64.62 kcal/mol
Dissociation entropy (TΔSdiss): 74.56 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-272344

Macromolecules

Spike glycoprotein E1
Chains: A, B, C, D, E, F
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%)
Pfam: Alphavirus E1 glycoprotein
Spike glycoprotein E1 in PDB entry 8deq, assembly 1, front view.
Spike glycoprotein E1 in PDB entry 8deq, assembly 1, side view.
Spike glycoprotein E1 in PDB entry 8deq, assembly 1, top view.
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SKV09 Fab Heavy Chain
Chain: H
Length: 120 amino acids
Theoretical weight: 13.1 KDa
Source organism: Macaca
Expression system: Homo sapiens
SKV09 Fab Heavy Chain in PDB entry 8deq, assembly 1, front view.
SKV09 Fab Heavy Chain in PDB entry 8deq, assembly 1, side view.
SKV09 Fab Heavy Chain in PDB entry 8deq, assembly 1, top view.
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SKV09 Fab Light Chain
Chain: L
Length: 107 amino acids
Theoretical weight: 11.76 KDa
Source organism: Macaca
Expression system: Homo sapiens
SKV09 Fab Light Chain in PDB entry 8deq, assembly 1, front view.
SKV09 Fab Light Chain in PDB entry 8deq, assembly 1, side view.
SKV09 Fab Light Chain in PDB entry 8deq, assembly 1, top view.
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