5Z0V | pdb_00005z0v

Structural insight into the Zika virus capsid encapsulating the viral genome

• PDB DOI: https://doi.org/10.2210/pdb5Z0V/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia coli BL21(DE3), Zika virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-12-21 Released: 2018-04-11 
• Deposition Author(s): Li, T., Zhao, Q., Yang, X., Chen, C., Yang, K., Wu, C., Zhang, T., Duan, Y., Xue, X., Mi, K., Ji, X., Wang, Z., Yang, H.
• Funding Organization(s): the National Key Basic Research Program of China, the National Natural Science Foundation of China, the National Key Research Program of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Models: experimental

Literature

Structural insight into the Zika virus capsid encapsulating the viral genome.

Li, T., Zhao, Q., Yang, X., Chen, C., Yang, K., Wu, C., Zhang, T., Duan, Y., Xue, X., Mi, K., Ji, X., Wang, Z., Yang, H.

(2018) Cell Res 28: 497-499

• PubMed: 29467384 
• DOI: https://doi.org/10.1038/s41422-018-0007-9
• Primary Citation Related Structures: 
  5Z0R, 5Z0V

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Organizational Affiliation: 
• School of Life Sciences, Tianjin University, Tianjin, 300072, China.
Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China.
School of Life Sciences, Tianjin University, Tianjin, 300072, China. [e-mail].
Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 197.28 kDa 
• Atom Count: 13,947 
• Modeled Residue Count: 1,769 
• Deposited Residue Count: 1,780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein family 1,viral genome protein	A, B, C, D	445	Escherichia coli BL21(DE3), Zika virus This entity is chimeric	Mutation(s): 1  Gene Names: ECBD_4002
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1  Go to UniProtKB:  Q32ZE1
UniProt Groups	P0AEX9Q32ZE1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	E, F, G, H	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.104	α = 90
b = 223.076	β = 109.99
c = 85.165	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: 2018-04-11 
Deposition Author(s): Li, T., Zhao, Q., Yang, X., Chen, C., Yang, K., Wu, C., Zhang, T., Duan, Y., Xue, X., Mi, K., Ji, X., Wang, Z., Yang, H.

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Funding Organization	Location	Grant Number
the National Key Basic Research Program of China	China	2015CB859800
the National Natural Science Foundation of China	China	31528006
the National Key Research Program of China	China	2016YFD0500300

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2018-05-02
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary