7V3H | pdb_00007v3h

DENV2_NGC_Fab_C10 28degrees (3Fab:3E)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7V3H

This is version 1.2 of the entry. See complete history

Literature

Human antibody C10 neutralizes by diminishing Zika but enhancing dengue virus dynamics.

Lim, X.X.Shu, B.Zhang, S.Tan, A.W.K.Ng, T.S.Lim, X.N.Chew, V.S.Shi, J.Screaton, G.R.Lok, S.M.Anand, G.S.

(2021) Cell 184: 6067-6080.e13

  • DOI: https://doi.org/10.1016/j.cell.2021.11.009
  • Primary Citation Related Structures: 
    7V3F, 7V3G, 7V3H, 7V3I, 7V3J

  • PubMed Abstract: 

    The human monoclonal antibody (HmAb) C10 potently cross-neutralizes Zika virus (ZIKV) and dengue virus. Analysis of antibody fragment (Fab) C10 interactions with ZIKV and dengue virus serotype 2 (DENV2) particles by cryoelectron microscopy (cryo-EM) and amide hydrogen/deuterium exchange mass spectrometry (HDXMS) shows that Fab C10 binding decreases overall ZIKV particle dynamics, whereas with DENV2, the same Fab causes increased dynamics. Testing of different Fab C10:DENV2 E protein molar ratios revealed that, at higher Fab ratios, especially at saturated concentrations, the Fab enhanced viral dynamics (detected by HDXMS), and observation under cryo-EM showed increased numbers of distorted particles. Our results suggest that Fab C10 stabilizes ZIKV but that with DENV2 particles, high Fab C10 occupancy promotes E protein dimer conformational changes leading to overall increased particle dynamics and distortion of the viral surface. This is the first instance of a broadly neutralizing antibody eliciting virus-specific increases in whole virus particle dynamics.


  • Organizational Affiliation
    • Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.

Macromolecule Content 

  • Total Structure Weight: 265.61 kDa 
  • Atom Count: 18,610 
  • Modeled Residue Count: 2,409 
  • Deposited Residue Count: 2,409 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope protein EA [auth B],
C [auth A],
E [auth C]
495Dengue virus 2 Thailand/NGS-C/1944Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P14340 (Dengue virus type 2 (strain Thailand/NGS-C/1944))
Explore P14340 
Go to UniProtKB:  P14340
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14340
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Small envelope protein MB [auth E],
D,
F
72Dengue virus 2 Thailand/NGS-C/1944Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P14340 (Dengue virus type 2 (strain Thailand/NGS-C/1944))
Explore P14340 
Go to UniProtKB:  P14340
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14340
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
C10 IgG light chain variable regionG [auth I],
I [auth G],
K
127Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
C10 IgG heavy chain variable regionH [auth M],
J [auth H],
L
109Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth J]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF2017NRF-CRP001-027
National Research Foundation (NRF, Singapore)SingaporeNRF-NRFI2016-01
National Research Foundation (NRF, Singapore)SingaporeNRF2016NRF-CRP001-063

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection