PDBsum entry 3uaj

Viral protein/immune system

PDB id: 3uaj

Contents

Protein chains

371 a.a.

219 a.a.

213 a.a.

Ligands

NAG ×2

PDB id:

3uaj

Name:

Viral protein/immune system

Title:

Crystal structure of the envelope glycoprotein ectodomain from dengue virus serotype 4 in complex with the fab fragment of the chimpanzee monoclonal antibody 5h2

Structure:

Envelope protein. Chain: b, a. Fragment: unp residues 280-674. Engineered: yes. Heavy chain, monoclonal antibody 5h2. Chain: h, c. Fragment: fab. Engineered: yes. Light chain, monoclonal antibody 5h2.

Source:

Dengue virus 4. Organism_taxid: 11070. Strain: myanmar 1976. Gene: envelope. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227. Pan troglodytes. Chimpanzee. Organism_taxid: 9598.

Resolution:

3.23Å R-factor: 0.241 R-free: 0.247

Authors:

J.J.B.Cockburn,E.A.Stura,M.E.Navarro-Sanchez,F.A.Rey

Key ref:

J.J.Cockburn et al. (2012). Structural insights into the neutralization mechanism of a higher primate antibody against dengue virus. Embo J, 31, 767-779. PubMed id: 22139356

Date:

21-Oct-11 Release date: 14-Dec-11

Protein chains

P09866  (POLG_DEN4D) -  Genome polyprotein from Dengue virus type 4 (strain Dominica/814669/1981)

Seq: 3387 a.a.

Struc: 371 a.a.

Protein chains

No UniProt id for this chain

Struc: 219 a.a.

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Enzyme reactions

• Enzyme class 2: Chains B, A: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
• Enzyme class 3: Chains B, A: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺
• Enzyme class 4: Chains B, A: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 5: Chains B, A: E.C.3.4.21.91 - flavivirin.
• Reaction: Selective hydrolysis of Xaa-Xaa-|-Xbb bonds in which each of the Xaa can be either Arg or Lys and Xbb can be either Ser or Ala.
• Enzyme class 6: Chains B, A: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 7: Chains B, A: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = NAG) matches with 41.38% similarity) + phosphate + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Embo J 31:767-779 (2012)

PubMed id: 22139356

Structural insights into the neutralization mechanism of a higher primate antibody against dengue virus.

J.J.Cockburn, M.E.Navarro Sanchez, A.P.Goncalvez, E.Zaitseva, E.A.Stura, C.M.Kikuti, S.Duquerroy, P.Dussart, L.V.Chernomordik, C.J.Lai, F.A.Rey.

ABSTRACT

No abstract given.