PDBsum entry 4b03

Virus

PDB id: 4b03

Contents

Protein chains

495 a.a.*

166 a.a.*

* C-alpha coords only

PDB id:

4b03

Name:

Virus

Title:

6a electron cryomicroscopy structure of immature dengue virus serotype 1

Structure:

Dengue virus 1 e protein. Chain: a, b, c. Dengue virus 1 prm protein. Chain: d, e, f

Source:

Dengue virus 1. Organism_taxid: 11053. Strain: pvp159 (den1/sg/07k3640dk1/2008). Strain: pvp159 (den1/sg/07k3640dk1/2008)

Authors:

V.A.Kostyuchenko,Q.Zhang,L.C.Tan,T.S.Ng,S.M.Lok

Key ref:

V.A.Kostyuchenko et al. (2013). Immature and mature dengue serotype 1 virus structures provide insight into the maturation process. J Virol, 87, 7700-7707. PubMed id: 23637416 DOI: 10.1128/JVI.00197-13

Date:

28-Jun-12 Release date: 05-Jun-13

Protein chains

G3F5K5  (G3F5K5_9FLAV) -  Genome polyprotein from dengue virus type 1

Seq: 3392 a.a.

Struc: 495 a.a.*

Protein chains

G3F5K5  (G3F5K5_9FLAV) -  Genome polyprotein from dengue virus type 1

Seq: 3392 a.a.

Struc: 166 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D, E, F: 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 2: Chains A, B, C, D, E, F: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 3: Chains A, B, C, D, E, F: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + 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

DOI no: 10.1128/JVI.00197-13

J Virol 87:7700-7707 (2013)

PubMed id: 23637416

Immature and mature dengue serotype 1 virus structures provide insight into the maturation process.

V.A.Kostyuchenko, Q.Zhang, J.L.Tan, T.S.Ng, S.M.Lok.

ABSTRACT

Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, respectively. The subnanometer-resolution maps allow accurate placement of all of the surface proteins. Although the immature and mature viruses showed vastly different surface protein organizations, the envelope protein transmembrane (E-TM) regions remain in similar positions. The pivotal role of the E-TM regions leads to the identification of the start and end positions of all surface proteins during maturation.