7A3T | pdb_00007a3t

Crystal structure of dengue 3 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8

PDB DOI: https://doi.org/10.2210/pdb7A3T/pdb

Classification: VIRAL PROTEIN
Organism(s): dengue virus type 3, Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): Yes

Deposited: 2020-08-18 Released: 2021-12-08
Deposition Author(s): Sharma, A., Vaney, M.C., Guardado-Calvo, P., Duquerroy, S., Rouvinski, A., Rey, F.A.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.207 (Depositor), 0.209 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses.

Sharma, A., Zhang, X., Dejnirattisai, W., Dai, X., Gong, D., Wongwiwat, W., Duquerroy, S., Rouvinski, A., Vaney, M.C., Guardado-Calvo, P., Haouz, A., England, P., Sun, R., Zhou, Z.H., Mongkolsapaya, J., Screaton, G.R., Rey, F.A.

(2021) Cell 184: 6052-6066.e18

PubMed: 34852239 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2021.11.010
Primary Citation Related Structures:
7A3N, 7A3O, 7A3P, 7A3Q, 7A3R, 7A3S, 7A3T, 7A3U, 7CTH

PubMed Abstract:
The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative structure-function analysis of C10 bound to the envelope (E) protein dimers of the five viruses it neutralizes. We demonstrate that the C10 Fab has high affinity for ZIKV and DENV1 but not for DENV2, DENV3, and DENV4. We further show that the C10 interaction with the latter viruses requires an E protein conformational landscape that limits binding to only one of the three independent epitopes per virion. This limited affinity is nevertheless counterbalanced by the particle's icosahedral organization, which allows two different dimers to be reached by both Fab arms of a C10 immunoglobulin. The epitopes' geometric distribution thus confers C10 its exceptional neutralization breadth. Our results highlight the importance not only of paratope/epitope complementarity but also the topological distribution for epitope-focused vaccine design.

Organizational Affiliation

Institut Pasteur, Université de Paris, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France.

Institut Pasteur, Université de Paris, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France; Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518055, China.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.

Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.

Institut Pasteur, Université de Paris, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France; Université Paris-Saclay, Faculté des Sciences, F-91405 Orsay, France.

Institut Pasteur, Université de Paris, CNRS UMR 3528, Center for Technological Resources and Research, 75015 Paris, France.

Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.

Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.

Division of Medical Sciences, University of Oxford, Oxford, UK. Electronic address: gavin.screaton@medsci.ox.ac.uk.

Institut Pasteur, Université de Paris, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France. Electronic address: felix.rey@pasteur.fr.

Macromolecule Content

Total Structure Weight: 101.29 kDa
Atom Count: 6,403
Modeled Residue Count: 818
Deposited Residue Count: 917
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Core protein	A	428	dengue virus type 3	Mutation(s): 2 Gene Names: POLY EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P27915 (Dengue virus type 3 (strain Philippines/H87/1956)) Explore P27915 Go to UniProtKB: P27915
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27915
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EDE1 C8 antibody Fab fragment	B [auth H]	272	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EDE1 C8 antibody Fab fragment	C [auth L]	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	5		N-Glycosylation	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth H] SDF format, chain K [auth H] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H]	E [auth A], F [auth A], J [auth H], K [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth H] Focus chain K [auth H] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth H] Focus chain K [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L	G [auth A], H [auth A], I [auth A], L	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L