6NIP | pdb_00006nip

Crystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ1 in complex with ZIKV E glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb6NIP/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
• Expression System: Homo sapiens, Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2018-12-31 Released: 2019-12-25 
• Deposition Author(s): Sankhala, R.S., Dussupt, V., Donofrio, G., Choe, M., Modjarrad, K., Michael, N.L., Krebs, S.J., Joyce, M.G.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.16 Å
• R-Value Free: 
  0.237 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Models: experimental

Literature

Potent Zika and dengue cross-neutralizing antibodies induced by Zika vaccination in a dengue-experienced donor.

Dussupt, V., Sankhala, R.S., Gromowski, G.D., Donofrio, G., De La Barrera, R.A., Larocca, R.A., Zaky, W., Mendez-Rivera, L., Choe, M., Davidson, E., McCracken, M.K., Brien, J.D., Abbink, P., Bai, H., Bryan, A.L., Bias, C.H., Berry, I.M., Botero, N., Cook, T., Doria-Rose, N.A., Escuer, A.G.I., Frimpong, J.A., Geretz, A., Hernandez, M., Hollidge, B.S., Jian, N., Kabra, K., Leggat, D.J., Liu, J., Pinto, A.K., Rutvisuttinunt, W., Setliff, I., Tran, U., Townsley, S., Doranz, B.J., Rolland, M., McDermott, A.B., Georgiev, I.S., Thomas, R., Robb, M.L., Eckels, K.H., Barranco, E., Koren, M., Smith, D.R., Jarman, R.G., George, S.L., Stephenson, K.E., Barouch, D.H., Modjarrad, K., Michael, N.L., Joyce, M.G., Krebs, S.J.

(2020) Nat Med 26: 228-235

• PubMed: 32015557 
• DOI: https://doi.org/10.1038/s41591-019-0746-2
• Primary Citation Related Structures: 
  6MTX, 6MTY, 6NIP, 6NIS, 6NIU


• PubMed Abstract: 
  

  Zika virus (ZIKV) has caused significant disease, with widespread cases of neurological pathology and congenital neurologic defects. Rapid vaccine development has led to a number of candidates capable of eliciting potent ZIKV-neutralizing antibodies (reviewed in refs. ^1-3 ). Despite advances in vaccine development, it remains unclear how ZIKV vaccination affects immune responses in humans with prior flavivirus immunity. Here we show that a single-dose immunization of ZIKV purified inactivated vaccine (ZPIV) ^4-7 in a dengue virus (DENV)-experienced human elicited potent cross-neutralizing antibodies to both ZIKV and DENV. Using a unique ZIKV virion-based sorting strategy, we isolated and characterized multiple antibodies, including one termed MZ4, which targets a novel site of vulnerability centered on the Envelope (E) domain I/III linker region and protects mice from viremia and viral dissemination following ZIKV or DENV-2 challenge. These data demonstrate that Zika vaccination in a DENV-experienced individual can boost pre-existing flavivirus immunity and elicit protective responses against both ZIKV and DENV. ZPIV vaccination in Puerto Rican individuals with prior flavivirus experience yielded similar cross-neutralizing potency after a single vaccination, highlighting the potential benefit of ZIKV vaccination in flavivirus-endemic areas.

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Organizational Affiliation: 
• Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Viral Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Pilot Bioproduction Facility, Center for Enabling Capabilities, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Ragon Institute of MGH, Cambridge, MA, USA.
Integral Molecular, Philadelphia, PA, USA.
Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA.
Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.
U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA.
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.
Ponce Health Sciences University, CAIMED Center, Ponce, Puerto Rico, USA.
Immunodiagnostics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA.
Department of Internal Medicine, Division of Infectious Diseases, Allergy and Immunology, Saint Louis University School of Medicine and St Louis VA Medical Center, Saint Louis, MO, USA.
Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA. [e-mail].
U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA. [e-mail].
Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA. [e-mail].
Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA. [e-mail].
U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA. [e-mail].
Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 190.61 kDa 
• Atom Count: 12,632 
• Modeled Residue Count: 1,668 
• Deposited Residue Count: 1,776 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MZ1 Heavy chain	A, E [auth H]	225	Homo sapiens	Mutation(s): 0  Gene Names: IGHV4-59*08

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MZ1 Light Chain	B, F [auth L]	216	Homo sapiens	Mutation(s): 0  Gene Names: IGLV1-44*01

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	C [auth Z], D [auth E]	447	Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013	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: X-RAY DIFFRACTION
• Resolution: 4.16 Å
• R-Value Free:  0.237 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 417.33	α = 90
b = 69.3	β = 112.96
c = 212.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Sankhala, R.S., Dussupt, V., Donofrio, G., Choe, M., Modjarrad, K., Michael, N.L., Krebs, S.J., Joyce, M.G.

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Funding Organization	Location	Grant Number
Other government	United States	W81XWH-07-2-0067

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2021-01-06
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary