5UHY | pdb_00005uhy

A Human Antibody Against Zika Virus Crosslinks the E Protein to Prevent Infection

• PDB DOI: https://doi.org/10.2210/pdb5UHY/pdb
• EM Map EMD-8548: EMDB EMDataResource

• Classification: VIRUS/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Zika virus
• Expression System: Homo sapiens, Cricetinae gen. sp.
• Mutation(s): No 


• Deposited: 2017-01-12 Released: 2017-03-29 
• Deposition Author(s): Hasan, S.S., Miller, A., Sapparapu, G., Fernandez, E., Klose, T., Long, F., Fokine, A., Porta, J.C., Jiang, W., Diamond, M.S., Crowe Jr., J.E., Kuhn, R.J., Rossmann, M.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A human antibody against Zika virus crosslinks the E protein to prevent infection.

Hasan, S.S., Miller, A., Sapparapu, G., Fernandez, E., Klose, T., Long, F., Fokine, A., Porta, J.C., Jiang, W., Diamond, M.S., Crowe, J.E., Kuhn, R.J., Rossmann, M.G.

(2017) Nat Commun 8: 14722-14722

• PubMed: 28300075 
• DOI: https://doi.org/10.1038/ncomms14722
• Primary Citation Related Structures: 
  5UHY


• PubMed Abstract: 
  

  The recent Zika virus (ZIKV) epidemic has been linked to unusual and severe clinical manifestations including microcephaly in fetuses of infected pregnant women and Guillian-Barré syndrome in adults. Neutralizing antibodies present a possible therapeutic approach to prevent and control ZIKV infection. Here we present a 6.2 Å resolution three-dimensional cryo-electron microscopy (cryoEM) structure of an infectious ZIKV (strain H/PF/2013, French Polynesia) in complex with the Fab fragment of a highly therapeutic and neutralizing human monoclonal antibody, ZIKV-117. The antibody had been shown to prevent fetal infection and demise in mice. The structure shows that ZIKV-117 Fabs cross-link the monomers within the surface E glycoprotein dimers as well as between neighbouring dimers, thus preventing the reorganization of E protein monomers into fusogenic trimers in the acidic environment of endosomes.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.
The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.
Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
Markey Center for Structural Biology and Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, USA.
Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA.
Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, Missouri 63110, USA.
Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 420-mer - A180B120C120 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 420-mer - A180B180C60 

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

Macromolecule Content 

• Total Structure Weight: 222.84 kDa 
• Atom Count: 14,281 
• Modeled Residue Count: 2,052 
• Deposited Residue Count: 2,052 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZV67 Fab chain 1	A [auth G], C [auth I]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ZV67 Fab chain 2	B [auth H], D [auth J]	218	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
envelope protein	E [auth C], F [auth E], G [auth A]	396	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	jspr

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Hasan, S.S., Miller, A., Sapparapu, G., Fernandez, E., Klose, T., Long, F., Fokine, A., Porta, J.C., Jiang, W., Diamond, M.S., Crowe Jr., J.E., Kuhn, R.J., Rossmann, M.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI076331
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI073755
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI104972
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201400024C

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary