4C2I

Cryo-EM structure of Dengue virus serotype 1 complexed with Fab fragments of human antibody 1F4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A Potent Anti-Dengue Human Antibody Preferentially Recognizes the Conformation of E Protein Monomers Assembled on the Virus Surface.

Fibriansah, G.Tan, J.L.Smith, S.A.De Alwis, A.R.Ng, T.Kostyuchenko, V.A.Ibarra, K.D.Wang, J.Harris, E.De Silva, A.Crowe, J.E.J.Lok, S.

(2014) EMBO Mol Med 6: 358

  • DOI: 10.1002/emmm.201303404
  • Primary Citation of Related Structures:  
    4C2I

  • PubMed Abstract: 
  • Dengue virus (DENV), which consists of four serotypes (DENV1-4), infects over 400 million people annually. Previous studies have indicated most human monoclonal antibodies (HMAbs) from dengue patients are cross-reactive and poorly neutralizing. Rare neutralizing HMAbs are usually serotype-specific and bind to quaternary structure-dependent epitopes ...

    Dengue virus (DENV), which consists of four serotypes (DENV1-4), infects over 400 million people annually. Previous studies have indicated most human monoclonal antibodies (HMAbs) from dengue patients are cross-reactive and poorly neutralizing. Rare neutralizing HMAbs are usually serotype-specific and bind to quaternary structure-dependent epitopes. We determined the structure of DENV1 complexed with Fab fragments of a highly potent HMAb 1F4 to 6 Å resolution by cryo-EM. Although HMAb 1F4 appeared to bind to virus and not E proteins in ELISAs in the previous study, our structure showed that the epitope is located within an envelope (E) protein monomer, and not across neighboring E proteins. The Fab molecules bind to domain I (DI), and DI-DII hinge of the E protein. We also showed that HMAb 1F4 can neutralize DENV at different stages of viral entry in a cell type and receptor dependent manner. The structure reveals the mechanism by which this potent and specific antibody blocks viral infection.


    Organizational Affiliation

    Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore City, Singapore.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENVELOPE PROTEINA, C, E495Dengue virus 1Mutation(s): 0 
Gene Names: E
UniProt
Find proteins for Q7TGE4 (Dengue virus 1)
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Go to UniProtKB:  Q7TGE4
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UniProt GroupQ7TGE4
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
POLYPROTEINB, D, F75Dengue virus 1Mutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for G3F5K5 (Dengue virus 1)
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Go to UniProtKB:  G3F5K5
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UniProt GroupG3F5K5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4G [auth H],
I [auth M]
232Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4H [auth L],
J [auth N]
239Homo sapiensMutation(s): 0 
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth G],
N [auth K]
3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth I],
M [auth J],
O
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
P [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900017
Query on PRD_900017
K [auth G], N [auth K]triacetyl-beta-chitotrioseOligosaccharide / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Other, Source and taxonomy
  • Version 1.2: 2014-03-19
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Data collection, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary