Biological Assembly 1  

 3D View: Structure

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 240-mer - A180B60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 151.38 kDa 
• Atom Count: 1295 
• Residue Count: 1295 
• Unique protein chains: 2

2B6B

Cryo EM structure of Dengue complexed with CRD of DC-SIGN

• DOI: 10.2210/pdb2B6B/pdb
• EMDataResource: EMD-1166

• Classification: Virus/Receptor
• Organism(s): Dengue virus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-30 Released: 2006-03-07 
• Deposition Author(s): Pokidysheva, E., Zhang, Y., Battisti, A.J., Bator-Kelly, C.M., Chipman, P.R., Gregorio, G., Hendrickson, W.A., Kuhn, R.J., Rossmann, M.G.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 25.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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

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

(2006) Cell 124: 485-493

• PubMed: 16469696 
• DOI: 10.1016/j.cell.2005.11.042
• Primary Citation of Related Structures:  
  2B6B


• PubMed 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.

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Organizational Affiliation: 

Department of Biological Sciences, Lilly Hall, 915 W. State Street, Purdue University, West Lafayette, IN 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
envelope glycoprotein	A, B, C	394	Dengue virus	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
Find proteins for Q9WDA7 (Dengue virus 2) Explore Q9WDA7  Go to UniProtKB:  Q9WDA7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CD209 antigen	D	175	Homo sapiens	Mutation(s): 0  Gene Names: CD209, CLEC4L
Find proteins for Q9NNX6 (Homo sapiens) Explore Q9NNX6  Go to UniProtKB:  Q9NNX6
NIH Common Fund Data Resources
PHAROS:  Q9NNX6 GTEx:  ENSG00000090659

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 25.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-30 
• Released Date: 2006-03-07 
Deposition Author(s): Pokidysheva, E., Zhang, Y., Battisti, A.J., Bator-Kelly, C.M., Chipman, P.R., Gregorio, G., Hendrickson, W.A., Kuhn, R.J., Rossmann, M.G.

Revision History 

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-07-18
  Changes: Data collection