Biological Assembly 1  

 3D View: Structure

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 360-mer - A180B180 

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

Macromolecule Content

• Total Structure Weight: 190.10 kDa 
• Atom Count: 11024 
• Residue Count: 1728 
• Unique protein chains: 2

5IRE

The cryo-EM structure of Zika Virus

• DOI: 10.2210/pdb5IRE/pdb
• EMDataResource: EMD-8116

• Classification: VIRUS
• Organism(s): Zika virus
• Mutation(s): No 


• Deposited: 2016-03-13 Released: 2016-03-30 
• Deposition Author(s): Sirohi, D., Chen, Z., Sun, L., Klose, T., Pierson, T., Rossmann, M., Kuhn, R.
• 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: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The 3.8 angstrom resolution cryo-EM structure of Zika virus.

Sirohi, D., Chen, Z., Sun, L., Klose, T., Pierson, T.C., Rossmann, M.G., Kuhn, R.J.

(2016) Science 352: 467-470

• PubMed: 27033547 
• DOI: 10.1126/science.aaf5316
• Primary Citation of Related Structures:  
  5IRE


• PubMed Abstract: 
  

The recent rapid spread of Zika virus and its unexpected linkage to birth defects and an autoimmune neurological syndrome have generated worldwide concern. Zika virus is a flavivirus like the dengue, yellow fever, and West Nile viruses. We present the 3.8 angstrom resolution structure of mature Zika virus, determined by cryo-electron microscopy (cryo-EM). The structure of Zika virus is similar to other known flavivirus structures, except for the ~10 amino acids that surround the Asn(154) glycosylation site in each of the 180 envelope glycoproteins that make up the icosahedral shell. The carbohydrate moiety associated with this residue, which is recognizable in the cryo-EM electron density, may function as an attachment site of the virus to host cells. This region varies not only among Zika virus strains but also in other flaviviruses, which suggests that differences in this region may influence virus transmission and disease.

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Organizational Affiliation: 

Markey Center for Structural Biology and Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E protein	A, C, E	504	Zika virus	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)
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	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)
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	2		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-03-13 
• Released Date: 2016-03-30 
Deposition Author(s): Sirohi, D., Chen, Z., Sun, L., Klose, T., Pierson, T., Rossmann, M., Kuhn, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI073755
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI07633

Revision History 

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2016-04-06
  Changes: Other
• Version 1.2: 2016-05-04
  Changes: Derived calculations
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2018-07-18
  Changes: Data collection
• Version 1.5: 2019-12-11
  Changes: Author supporting evidence, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary