4UT7 | pdb_00004ut7

CRYSTAL STRUCTURE OF THE SCFV FRAGMENT OF THE BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11

• PDB DOI: https://doi.org/10.2210/pdb4UT7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2014-07-18 Released: 2015-01-28 
• Deposition Author(s): Rouvinski, A., Guardado-Calvo, P., Barba-Spaeth, G., Duquerroy, S., Vaney, M.C., Rey, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.191 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: other

Literature

Recognition Determinants of Broadly Neutralizing Human Antibodies Against Dengue Viruses.

Rouvinski, A., Guardado-Calvo, P., Barba-Spaeth, G., Duquerroy, S., Vaney, M., Kikuti, C.M., Navarro Sanchez, M.E., Dejnirattisai, W., Wongwiwat, W., Haouz, A., Girard-Blanc, C., Petres, S., Shepard, W.E., Despres, P., Arenzana-Seisdedos, F., Dussart, P., Mongkolsapaya, J., Screaton, G.R., Rey, F.A.

(2015) Nature 520: 109

• PubMed: 25581790 
• DOI: https://doi.org/10.1038/nature14130
• Primary Citation Related Structures: 
  4UT6, 4UT7, 4UT9, 4UTA, 4UTB, 4UTC


• PubMed Abstract: 
  

  Dengue disease is caused by four different flavivirus serotypes, which infect 390 million people yearly with 25% symptomatic cases and for which no licensed vaccine is available. Recent phase III vaccine trials showed partial protection, and in particular no protection for dengue virus serotype 2 (refs 3, 4). Structural studies so far have characterized only epitopes recognized by serotype-specific human antibodies. We recently isolated human antibodies potently neutralizing all four dengue virus serotypes. Here we describe the X-ray structures of four of these broadly neutralizing antibodies in complex with the envelope glycoprotein E from dengue virus serotype 2, revealing that the recognition determinants are at a serotype-invariant site at the E-dimer interface, including the exposed main chain of the E fusion loop and the two conserved glycan chains. This 'E-dimer-dependent epitope' is also the binding site for the viral glycoprotein prM during virus maturation in the secretory pathway of the infected cell, explaining its conservation across serotypes and highlighting an Achilles' heel of the virus with respect to antibody neutralization. These findings will be instrumental for devising novel immunogens to protect simultaneously against all four serotypes of dengue virus.

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Organizational Affiliation: 
• 1] Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France [2] CNRS UMR 3569 Virologie, 75724 Paris Cedex 15, France.
1] Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France [2] CNRS UMR 3569 Virologie, 75724 Paris Cedex 15, France [3] Université Paris-Sud, Faculté des Sciences, 91405 Orsay, France.
Division of Immunology and Inflammation, Department of Medicine, Hammersmith Hospital Campus, Imperial College London, London W12 0NN, UK.
Institut Pasteur, Protéopôle, CNRS UMR 3528, 75724 Paris Cedex 15, France.
Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP48, 91192 Gif-sur-Yvette, France.
Institut Pasteur, Département de Virologie, Unité des Interactions Moléculaires Flavivirus-Hôtes, 75724 Paris Cedex 15, France.
Institut Pasteur, Département de Virologie, Unité de Pathogénie Virale, INSERM U1108, 75724 Paris Cedex 15, France.
Institut Pasteur de Guyane, BP 6010, 97306 Cayenne, French Guiana.
1] Division of Immunology and Inflammation, Department of Medicine, Hammersmith Hospital Campus, Imperial College London, London W12 0NN, UK [2] Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
1] Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France [2] CNRS UMR 3569 Virologie, 75724 Paris Cedex 15, France [3] Institut Pasteur, Protéopôle, CNRS UMR 3528, 75724 Paris Cedex 15, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 31.7 kDa 
• Atom Count: 2,220 
• Modeled Residue Count: 259 
• Deposited Residue Count: 303 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11	A [auth H]	150	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11	B [auth L]	153	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.191 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.92	α = 90
b = 47.67	β = 102.39
c = 90.67	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Rouvinski, A., Guardado-Calvo, P., Barba-Spaeth, G., Duquerroy, S., Vaney, M.C., Rey, F.A.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary