› 4ut6

X-ray diffraction
3.2Å resolution

Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 B7

Released:
DOI: 10.2210/pdb4ut6/pdb
PDB entry 4ut6 coloured by chain, front view.
PDB entry 4ut6 coloured by chain, side view.
PDB entry 4ut6 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-207257 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 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 B7 Chains: H, I
Molecule details ›
Chains: H, I
Length: 283 amino acids
Theoretical weight: 30.16 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
Structure domains: Immunoglobulins
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 Chains: L, M
Molecule details ›
Chains: L, M
Length: 218 amino acids
Theoretical weight: 22.96 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
1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P2
Unit cell:
a: 101.277Å b: 58.98Å c: 191.573Å
α: 90° β: 96.2° γ: 90°
R-values:
R R work R free
0.214 0.212 0.25
Expression system: Drosophila melanogaster

Quick links

Citations

62 review citations

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

13 mentions without citation

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