6IDI

Cryo-EM structure of Immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 8.0.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody.

Wirawan, M.Fibriansah, G.Marzinek, J.K.Lim, X.X.Ng, T.S.Sim, A.Y.L.Zhang, Q.Kostyuchenko, V.A.Shi, J.Smith, S.A.Verma, C.S.Anand, G.Crowe Jr., J.E.Bond, P.J.Lok, S.M.

(2019) Structure 27: 253-267.e8

  • DOI: 10.1016/j.str.2018.10.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti-precursor membrane (prM) protein antibodies. It is unk ...

    Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti-precursor membrane (prM) protein antibodies. It is unknown how anti-prM antibody-coated particles can undergo membrane fusion since the prM caps the envelope (E) protein fusion loop. Here, we determined cryoelectron microscopy (cryo-EM) maps of the immDENV:anti-prM complex at different pH values, mimicking the extracellular (pH 8.0) or endosomal (pH 5.0) environments. At pH 5.0, there are two structural classes with fewer antibodies bound than at pH 8.0. These classes may represent different maturation states. Molecular simulations, together with the measured high-affinity pr:antibody interaction (versus the weak pr:E interaction) and also the low pH cryo-EM structures, suggest how antibody:pr complex can dislodge from the E protein at low pH. This exposes the E protein fusion loop enhancing virus interaction with endosomes.


    Organizational Affiliation

    The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Departments of Pediatrics and Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: james.crowe@vanderbilt.edu.,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.,Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.,Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore.,Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, TN 37232, USA; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore. Electronic address: sheemei.lok@duke-nus.edu.sg.,Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.,Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore. Electronic address: peterjb@bii.a-star.edu.sg.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope protein
A, B, C
493Dengue virus 3Mutation(s): 0 
Find proteins for A9LID6 (Dengue virus 3)
Go to UniProtKB:  A9LID6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Premembrane protein
D, E, F
166Dengue virus 3Mutation(s): 0 
Find proteins for A9LID6 (Dengue virus 3)
Go to UniProtKB:  A9LID6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab 1H10 heavy chain (V-region)
H, I, M
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab 1H10 light chain (V-region)
J, L, N
116N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)SingaporeNRF-NRFI2016-01
Ministry of Education (Singapore)SingaporeMOE2012-T3-008
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesU54 AI057157
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesK08 AI103038

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references
  • Version 1.2: 2019-03-13
    Type: Data collection, Derived calculations