Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 360-mer - A180B180 

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

Macromolecule Content

• Total Structure Weight: 186.09 kDa 
• Atom Count: 1695 
• Modelled Residue Count: 1695 
• Deposited Residue Count: 1704 
• Unique protein chains: 2

3J6T

Cryo-EM structure of Dengue virus serotype 3 at 37 degrees C

• PDB DOI: 10.2210/pdb3J6T/pdb
• EM Map EMD-5934: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Dengue virus 3
• Expression System: Aedes albopictus
• Mutation(s): No 


• Deposited: 2014-03-25 Released: 2015-03-04 
• Deposition Author(s): Fibriansah, G., Tan, J.L., Smith, S.A., de Alwis, R., Ng, T.-S., Kostyuchenko, V.A., Kukkaro, P., de Silva, A.M., Crowe Jr., J.E., Lok, S.-M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins.

Fibriansah, G., Tan, J.L., Smith, S.A., de Alwis, R., Ng, T.S., Kostyuchenko, V.A., Jadi, R.S., Kukkaro, P., de Silva, A.M., Crowe, J.E., Lok, S.M.

(2015) Nat Commun 6: 6341-6341

• PubMed: 25698059 
• DOI: 10.1038/ncomms7341
• Primary Citation of Related Structures:  
  3J6S, 3J6T, 3J6U


• PubMed Abstract: 
  

Dengue virus (DENV) infects ~400 million people annually. There is no licensed vaccine or therapeutic drug. Only a small fraction of the total DENV-specific antibodies in a naturally occurring dengue infection consists of highly neutralizing antibodies. Here we show that the DENV-specific human monoclonal antibody 5J7 is exceptionally potent, neutralizing 50% of virus at nanogram-range antibody concentration. The 9 Å resolution cryo-electron microscopy structure of the Fab 5J7-DENV complex shows that a single Fab molecule binds across three envelope proteins and engages three functionally important domains, each from a different envelope protein. These domains are critical for receptor binding and fusion to the endosomal membrane. The ability to bind to multiple domains allows the antibody to fully coat the virus surface with only 60 copies of Fab, that is, half the amount compared with other potent antibodies. Our study reveals a highly efficient and unusual mechanism of molecular recognition by an antibody.

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Organizational Affiliation: 

1] Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore [2] Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
envelope protein	A, C, E	493	Dengue virus 3	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for A9LID6 (Dengue virus 3) Explore A9LID6  Go to UniProtKB:  A9LID6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
membrane protein	B, D, F	75	Dengue virus 3	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for A9LID6 (Dengue virus 3) Explore A9LID6  Go to UniProtKB:  A9LID6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-03-25 
• Released Date: 2015-03-04 
Deposition Author(s): Fibriansah, G., Tan, J.L., Smith, S.A., de Alwis, R., Ng, T.-S., Kostyuchenko, V.A., Kukkaro, P., de Silva, A.M., Crowe Jr., J.E., Lok, S.-M.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection