› 4ut9

X-ray diffraction
3.2Å resolution

Crystal structure of dengue 2 virus envelope glycoprotein dimer in complex with the ScFv fragment of the broadly neutralizing human antibody EDE1 C10

Released:
DOI: 10.2210/pdb4ut9/pdb
PDB entry 4ut9 coloured by chain, front view.
PDB entry 4ut9 coloured by chain, side view.
PDB entry 4ut9 coloured by chain, top view.
Source organisms:
Primary publication:
Recognition determinants of broadly neutralizing human antibodies against dengue viruses.
Rouvinski A, Guardado-Calvo P, Barba-Spaeth G, Duquerroy S, Vaney MC, Kikuti CM, Navarro Sanchez ME, Dejnirattisai W, Wongwiwat W, Haouz A, Girard-Blanc C, Petres S, Shepard WE, Desprès P, Arenzana-Seisdedos F, Dussart P, Mongkolsapaya J, Screaton GR, Rey FA
Nature 520 109-13 (2015)
PMID: 25581790

Function and Biology Details

Reactions catalysed: 
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212343 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
ENVELOPE GLYCOPROTEIN E Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 425 amino acids
Theoretical weight: 47.23 KDa
Source organism: dengue virus type 2
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q68Y26 (Residues: 281-671; Coverage: 12%)
Sequence domains:
Structure domains:
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C10 Chains: H, I, J, K
Molecule details ›
Chains: H, I, J, K
Length: 144 amino acids
Theoretical weight: 15.68 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
Structure domains: Immunoglobulins
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C10 Chains: L, M, N, O
Molecule details ›
Chains: L, M, N, O
Length: 154 amino acids
Theoretical weight: 15.63 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand NAG 4 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P1
Unit cell:
a: 57.522Å b: 102.235Å c: 131.092Å
α: 88.52° β: 85.69° γ: 83.9°
R-values:
R R work R free
0.2 0.198 0.249
Expression system: Drosophila melanogaster

Quick links

Citations

63 review citations

Exploitation of glycosylation in enveloped virus pathobiology.
Watanabe et al. (2019)
62 more

13 mentions without citation

Mapping the diverse structural landscape of the flavivirus antibody repertoire.
Sevvana et al. (2020)
12 more