6MID

Cryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195

• PDB DOI:  https://doi.org/10.2210/pdb6MID/pdb
• EM Map EMD-9131: EMDB EMDataResource

• Classification: VIRUS/IMMUNE SYSTEM
• Organism(s): Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013, Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMMemProtMD


• Deposited: 2018-09-19 Released: 2019-01-16 
• Deposition Author(s): Long, F., Rossmann, M.G.
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of a potent human monoclonal antibody against Zika virus targeting a quaternary epitope.

Long, F., Doyle, M., Fernandez, E., Miller, A.S., Klose, T., Sevvana, M., Bryan, A., Davidson, E., Doranz, B.J., Kuhn, R.J., Diamond, M.S., Crowe Jr., J.E., Rossmann, M.G.

(2019) Proc Natl Acad Sci U S A 116: 1591-1596

• PubMed: 30642974 
• DOI: https://doi.org/10.1073/pnas.1815432116
• Primary Citation of Related Structures:  
  6MID


• PubMed Abstract: 
  

Zika virus (ZIKV) is a major human pathogen and member of the Flavivirus genus in the Flaviviridae family. In contrast to most other insect-transmitted flaviviruses, ZIKV also can be transmitted sexually and from mother to fetus in humans. During recent outbreaks, ZIKV infections have been linked to microcephaly, congenital disease, and Guillain-Barré syndrome. Neutralizing antibodies have potential as therapeutic agents. We report here a 4-Å-resolution cryo-electron microscopy structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195. The footprint of the ZIKV-195 Fab fragment expands across two adjacent envelope (E) protein protomers. ZIKV neutralization by this antibody is presumably accomplished by cross-linking the E proteins, which likely prevents formation of E protein trimers required for fusion of the viral and cellular membranes. A single dose of ZIKV-195 administered 5 days after virus inoculation showed marked protection against lethality in a stringent mouse model of infection.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, IN 47907; [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 480-mer - A180B180C60D60 Pseudo Symmetry: Icosahedral - I  (3D View)
Pseudo Stoichiometry: Hetero 480-mer - A180B180C120 

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

Macromolecule Content

• Total Structure Weight: 216 kDa 
• Atom Count: 15,055 
• Modelled Residue Count: 1,965 
• Deposited Residue Count: 1,975 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E protein	A, C, E	504	Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M protein	B, D, F	75	Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
monoclonal antibody ZIKV-195 heavy chain	G [auth H]	128	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
monoclonal antibody ZIKV-195 light chain	H [auth L]	110	Homo sapiens	Mutation(s): 0  Gene Names: IGLV1-36 Membrane Entity: Yes
UniProt
Find proteins for A0A0B4J1U3 (Homo sapiens) Explore A0A0B4J1U3  Go to UniProtKB:  A0A0B4J1U3

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G], J [auth I], K [auth J]	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	jspr
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Long, F., Rossmann, M.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	AI076331

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2019-02-13
  Changes: Data collection, Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary