› 6epk

X-ray diffraction
2.7Å resolution

CRYSTAL STRUCTURE OF THE PRECURSOR MEMBRANE PROTEIN-ENVELOPE PROTEIN HETERODIMER FROM THE YELLOW FEVER VIRUS

Released:
DOI: 10.2210/pdb6epk/pdb
PDB entry 6epk coloured by chain, front view.
PDB entry 6epk coloured by chain, side view.
PDB entry 6epk coloured by chain, top view.
Source organism: Yellow fever virus
Primary publication:
New insight into flavivirus maturation from structure/function studies of the yellow fever virus envelope protein complex
Crampon E, Covernton E, Vaney MC, Dellarole M, Sommer S, Sharma A, Haouz A, England P, Lepault J, Duquerroy S, Rey FA, Barba-Spaeth G
MBio (2023)

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136778 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (5 distinct):
Envelope protein E Chains: A, D
Molecule details ›
Chains: A, D
Length: 427 amino acids
Theoretical weight: 46.32 KDa
Source organism: Yellow fever virus
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q6DV88 (Residues: 286-677; Coverage: 12%)
Sequence domains:
Structure domains:
Peptide pr Chains: B, E
Molecule details ›
Chains: B, E
Length: 89 amino acids
Theoretical weight: 10.19 KDa
Source organism: Yellow fever virus
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: P03314 (Residues: 122-210; Coverage: 3%)
Sequence domains: Flavivirus polyprotein propeptide

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
2 bound ligands:
Ligand SO4 23 x SO4
Ligand GOL 13 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P41
Unit cell:
a: 99.88Å b: 99.88Å c: 238.824Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.162 0.186
Expression system: Drosophila melanogaster

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