PDBsum entry 2b6b

Virus/receptor

PDB id: 2b6b

Contents

Protein chains

389 a.a.*

128 a.a.* *

* Residue conservation analysis

* C-alpha coords only

PDB id:

2b6b

Name:

Virus/receptor

Title:

Cryo em structure of dengue complexed with crd of dc-sign

Structure:

Envelope glycoprotein. Chain: a, b, c. Cd209 antigen. Chain: d. Synonym: dendritic cell-specific icam-3-grabbing nonintegrin 1, dc- sign1, dc-sign. Engineered: yes

Source:

Dengue virus. Organism_taxid: 12637. Homo sapiens. Human. Organism_taxid: 9606. Gene: cd209. Expressed in: escherichia coli. Expression_system_taxid: 562

Authors:

E.Pokidysheva,Y.Zhang,A.J.Battisti,C.M.Bator-Kelly,P.R.Chipman, G.Gregorio,W.A.Hendrickson,R.J.Kuhn,M.G.Rossmann

Key ref:

E.Pokidysheva et al. (2006). Cryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN. Cell, 124, 485-493. PubMed id: 16469696 DOI: 10.1016/j.cell.2005.11.042

Date:

30-Sep-05 Release date: 07-Mar-06

Protein chains

Q9WDA7  (Q9WDA7_9FLAV) -  Genome polyprotein from dengue virus type 2

Seq: 3391 a.a.

Struc: 389 a.a.*

Protein chain

Q9NNX6  (CD209_HUMAN) -  CD209 antigen from Homo sapiens

Seq: 404 a.a.

Struc: 128 a.a.

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

Enzyme reactions

• Enzyme class 1: Chains A, B, C: 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: 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: 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: 10.1016/j.cell.2005.11.042

Cell 124:485-493 (2006)

PubMed id: 16469696

Cryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN.

E.Pokidysheva, Y.Zhang, A.J.Battisti, C.M.Bator-Kelly, P.R.Chipman, C.Xiao, G.G.Gregorio, W.A.Hendrickson, R.J.Kuhn, M.G.Rossmann.

ABSTRACT

Dengue virus (DENV) is a significant human pathogen that causes millions of infections and results in about 24,000 deaths each year. Dendritic cell-specific ICAM3 grabbing nonintegrin (DC-SIGN), abundant in immature dendritic cells, was previously reported as being an ancillary receptor interacting with the surface of DENV. The structure of DENV in complex with the carbohydrate recognition domain (CRD) of DC-SIGN was determined by cryo-electron microscopy at 25 A resolution. One CRD monomer was found to bind to two glycosylation sites at Asn67 of two neighboring glycoproteins in each icosahedral asymmetric unit, leaving the third Asn67 residue vacant. The vacancy at the third Asn67 site is a result of the nonequivalence of the glycoprotein environments, leaving space for the primary receptor binding to domain III of E. The use of carbohydrate moieties for receptor binding sites suggests a mechanism for avoiding immune surveillance.

Selected figure(s)

Figure 1.
Figure 1. Structure of DC-SIGN

Figure 3.
Figure 3. Diagrammatic Representation of a DC-SIGN Tetrameric Molecule Interacting with the DENV Surface

The above figures are reprinted by permission from Cell Press: Cell (2006, 124, 485-493) copyright 2006.

Figures were selected by an automated process.