5VIG | pdb_00005vig

Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII

• PDB DOI: https://doi.org/10.2210/pdb5VIG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Zika virus
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-16 Released: 2017-05-03 
• Deposition Author(s): Keeffe, J.R., West Jr., A.P., Gristick, H.B., Bjorkman, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Recurrent Potent Human Neutralizing Antibodies to Zika Virus in Brazil and Mexico.

Robbiani, D.F., Bozzacco, L., Keeffe, J.R., Khouri, R., Olsen, P.C., Gazumyan, A., Schaefer-Babajew, D., Avila-Rios, S., Nogueira, L., Patel, R., Azzopardi, S.A., Uhl, L.F.K., Saeed, M., Sevilla-Reyes, E.E., Agudelo, M., Yao, K.H., Golijanin, J., Gristick, H.B., Lee, Y.E., Hurley, A., Caskey, M., Pai, J., Oliveira, T., Wunder, E.A., Sacramento, G., Nery, N., Orge, C., Costa, F., Reis, M.G., Thomas, N.M., Eisenreich, T., Weinberger, D.M., de Almeida, A.R.P., West, A.P., Rice, C.M., Bjorkman, P.J., Reyes-Teran, G., Ko, A.I., MacDonald, M.R., Nussenzweig, M.C.

(2017) Cell 169: 597-609.e11

• PubMed: 28475892 
• DOI: https://doi.org/10.1016/j.cell.2017.04.024
• Primary Citation Related Structures: 
  5VIC, 5VIG


• PubMed Abstract: 
  

  Antibodies to Zika virus (ZIKV) can be protective. To examine the antibody response in individuals who develop high titers of anti-ZIKV antibodies, we screened cohorts in Brazil and Mexico for ZIKV envelope domain III (ZEDIII) binding and neutralization. We find that serologic reactivity to dengue 1 virus (DENV1) EDIII before ZIKV exposure is associated with increased ZIKV neutralizing titers after exposure. Antibody cloning shows that donors with high ZIKV neutralizing antibody titers have expanded clones of memory B cells that express the same immunoglobulin VH3-23/VK1-5 genes. These recurring antibodies cross-react with DENV1, but not other flaviviruses, neutralize both DENV1 and ZIKV, and protect mice against ZIKV challenge. Structural analyses reveal the mechanism of recognition of the ZEDIII lateral ridge by VH3-23/VK1-5 antibodies. Serologic testing shows that antibodies to this region correlate with serum neutralizing activity to ZIKV. Thus, high neutralizing responses to ZIKV are associated with pre-existing reactivity to DENV1 in humans.

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Organizational Affiliation: 
• Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA. Electronic address: [e-mail].
Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil.
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.
National Institute of Respiratory Diseases, Mexico City CP 14080, Mexico.
Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA.
Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA; Faculdade de Medicina da Bahia and Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia CEP 40296-710, Brazil.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA.
Faculdade de Medicina da Bahia and Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia CEP 40296-710, Brazil.
Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA. Electronic address: [e-mail].
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 121.1 kDa 
• Atom Count: 7,905 
• Modeled Residue Count: 1,050 
• Deposited Residue Count: 1,110 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	A [auth H], D [auth A]	232	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6B291 (Homo sapiens) Explore S6B291  Go to UniProtKB:  S6B291

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	B [auth L], E [auth B]	213	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX7 (Homo sapiens) Explore P0DOX7  Go to UniProtKB:  P0DOX7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zika virus envelope protein DIII	C [auth Z], F [auth G]	110	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A192GPS0 (Zika virus) Explore A0A192GPS0  Go to UniProtKB:  A0A192GPS0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	G [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 385.082	α = 90
b = 385.082	β = 90
c = 56.64	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Keeffe, J.R., West Jr., A.P., Gristick, H.B., Bjorkman, P.J.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-17
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary