4UIF | pdb_00004uif

Cryo-EM structure of Dengue virus serotype 2 in complex with antigen-binding fragments of human antibody 2D22

• PDB DOI: https://doi.org/10.2210/pdb4UIF/pdb
• EM Map EMD-2967: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): dengue virus type 2, Homo sapiens
• Expression System: Aedes albopictus
• Mutation(s): No 


• Deposited: 2015-03-30 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 Junior, J.E., Lok, S.-M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

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: https://doi.org/10.1126/science.aaa8651
• Primary Citation 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.
Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA.
Department of Medicine, Vanderbilt University, Nashville, TN, USA. The Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.
Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
The Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA. Departments of Pediatrics and Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, USA. [e-mail] [e-mail].
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].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 720-mer - A180B180C180D180 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
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: 2,394 
• Modeled Residue Count: 2,394 
• Deposited Residue Count: 2,430 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DENGUE VIRUS SEROTYPE 2 STRAIN PVP94 07 - ENVELOPE PROTEIN	A, C, E	495	dengue virus type 2	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for E0WXJ2 (Dengue virus type 2) Explore E0WXJ2  Go to UniProtKB:  E0WXJ2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DENGUE VIRUS SEROTYPE 2 STRAIN STRAIN PVP94 07 - MEMBRANE PROTEIN	B, D, F	72	dengue virus type 2	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for E0WXJ2 (Dengue virus type 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
UniProt
Find proteins for S6BGD6 (Homo sapiens) Explore S6BGD6  Go to UniProtKB:  S6BGD6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN	1
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	MPSA

Structure Validation

Entry History 

Deposition Data

• 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 Junior, J.E., Lok, S.-M.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Data collection, Derived calculations
• Version 1.2: 2018-02-07
  Changes: Database references, Structure summary
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Refinement description