› 4utb

X-ray diffraction
3.85Å resolution

Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11

Released:
DOI: 10.2210/pdb4utb/pdb
PDB entry 4utb coloured by chain, front view.
PDB entry 4utb coloured by chain, side view.
PDB entry 4utb 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

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-493049 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
ENVELOPE GLYCOPROTEIN E Chains: A, B
Molecule details ›
Chains: A, B
Length: 422 amino acids
Theoretical weight: 46.82 KDa
Source organism: dengue virus type 2
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: A0A0B4SHY9 (Residues: 167-557; Coverage: 70%)
Sequence domains:
Structure domains:
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 Chains: H, I
Molecule details ›
Chains: H, I
Length: 283 amino acids
Theoretical weight: 30.36 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
Structure domains: Immunoglobulins
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 Chains: L, M
Molecule details ›
Chains: L, M
Length: 218 amino acids
Theoretical weight: 23.11 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 1 x NAG
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 58.779Å b: 181.85Å c: 204.823Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.23 0.257
Expression system: Drosophila melanogaster

Quick links

Citations

65 review citations

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

11 mentions without citation

Viral Membrane Fusion: A Dance Between Proteins and Lipids.
White et al. (2023)
10 more