5IRE

The cryo-EM structure of Zika Virus


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E protein
A, C, E
504Zika virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024B7W1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
M protein
B, D, F
75Zika virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024B7W1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.10.1-2155
RECONSTRUCTIONjspr2015

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI073755
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI07633

Revision History  (Full details and data files)

  • 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