Biological Assembly 1  

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

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 720-mer - A180B180C180D180 Pseudo Symmetry: Icosahedral - I  (3D View)
Pseudo Stoichiometry: Hetero 720-mer - A360B180C180 

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

Macromolecule Content

• Total Structure Weight: 264.79 kDa 
• Atom Count: 2394 
• Modelled Residue Count: 2394 
• Deposited Residue Count: 2430 
• Unique protein chains: 4

5A1Z

Cryo-EM structure of Dengue virus serotype 2 strain PVP94-07 complexed with human antibody 2D22 Fab at 37 degrees C

• PDB DOI: 10.2210/pdb5A1Z/pdb
• EM Map EMD-2996: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Dengue virus 2, Homo sapiens
• Expression System: Aedes albopictus
• Mutation(s): No 


• Deposited: 2015-05-06 Released: 2015-07-15 
• Deposition Author(s): Fibriansah, G., Ibarra, K.D., Ng, T.S., Smith, S.A., Tan, J.L., Lim, X.N., Ooi, J.S.G., Kostyuchenko, V.A., Wang, J., de Silva, A.M., Harris, E., Crowe Jr, J.E., Lok, S.M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers.

Fibriansah, G., Ibarra, K.D., Ng, T.S., Smith, S.A., Tan, J.L., Lim, X.N., Ooi, J.S., Kostyuchenko, V.A., Wang, J., de Silva, A.M., Harris, E., Crowe, J.E., Lok, S.M.

(2015) Science 349: 88-91

• PubMed: 26138979 
• DOI: 10.1126/science.aaa8651
• Primary Citation of Related Structures:  
  4UIF, 4UIH, 5A1Z


• PubMed Abstract: 
  

There are four closely-related dengue virus (DENV) serotypes. Infection with one serotype generates antibodies that may cross-react and enhance infection with other serotypes in a secondary infection. We demonstrated that DENV serotype 2 (DENV2)-specific human monoclonal antibody (HMAb) 2D22 is therapeutic in a mouse model of antibody-enhanced severe dengue disease. We determined the cryo-electron microscopy (cryo-EM) structures of HMAb 2D22 complexed with two different DENV2 strains. HMAb 2D22 binds across viral envelope (E) proteins in the dimeric structure, which probably blocks the E protein reorganization required for virus fusion. HMAb 2D22 "locks" two-thirds of or all dimers on the virus surface, depending on the strain, but neutralizes these DENV2 strains with equal potency. The epitope defined by HMAb 2D22 is a potential target for vaccines and therapeutics.

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Organizational Affiliation: 

Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, Singapore. Centre for BioImaging Sciences, National University of Singapore, Singapore. [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE PROTEIN	A, C, E	495	Dengue virus 2	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for E0WXJ2 (Dengue virus 2) Explore E0WXJ2  Go to UniProtKB:  E0WXJ2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MEMBRANE GLYCOPROTEIN	B, D, F	72	Dengue virus 2	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for E0WXJ2 (Dengue virus 2) Explore E0WXJ2  Go to UniProtKB:  E0WXJ2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN	G, I, K	128	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN	H, J, L	115	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-05-06 
• Released Date: 2015-07-15 
Deposition Author(s): Fibriansah, G., Ibarra, K.D., Ng, T.S., Smith, S.A., Tan, J.L., Lim, X.N., Ooi, J.S.G., Kostyuchenko, V.A., Wang, J., de Silva, A.M., Harris, E., Crowe Jr, J.E., Lok, S.M.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Other
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2018-02-07
  Changes: Database references