7F0H | pdb_00007f0h

Structural and functional characterization of bovine G1P[5] rotavirus VP8* protein

• PDB DOI: https://doi.org/10.2210/pdb7F0H/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Rotavirus A
• Expression System: Escherichia phage Ecwhy_1
• Mutation(s): No 


• Deposited: 2021-06-04 Released: 2021-12-29 
• Deposition Author(s): Duan, Z., Sun, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structural and functional characterization of bovine G1P[5] rotavirus VP8* protein.

Dang, L., Su, Y., Qi, J., Wu, Z., Li, D., Wang, M., Zhang, Q., Wang, H., Bai, R., Duan, Z., Sun, X.

(2021) Virology 563: 116-125

• PubMed: 34509703 
• DOI: https://doi.org/10.1016/j.virol.2021.08.009
• Primary Citation Related Structures: 
  7F0H


• PubMed Abstract: 
  

  The widely used rotavirus (RV) vaccine, Rotateq, contained reassortment strains of human and bovine G1/2/3/4P[5] RVs. The functional and structural features of bovine G1P[5] VP8* were investigated. Bovine G1P[5] VP8* was identified to interact with sialic acids and sialic acid-containing glycans. In addition, P[5] VP8* recognized α-Gal histo-blood group antigens (HBGAs). Bovine G1P[5] VP8* did not hemagglutinate the tested red blood cells. The crystal structure of P[5] VP8* was determined at 1.7 Å. Structural superimposition revealed that P[5] VP8* was most close to human P[8] VP8*, while much further to VP8*s of porcine P[7] and rhesus P[3]. Sequence alignment showed that amino acids of the putative glycan binding site in P[5] VP8* were different to those in P[3]/P[7] VP8*s, indicating that P[5] VP8* may interact with glycans using different mechanism. This study provided more understanding of P[5] RV infection and the interactions of RV VP8* and glycans.

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Organizational Affiliation: 
• National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, 102206, China; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China; Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot, 010059, China.
National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, 102206, China; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China.
Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
Inner Mongolia Medical University, Hohhot, 010059, China.
National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, 102206, China; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China. Electronic address: [e-mail].
National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, 102206, China; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China. Electronic address: [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

Macromolecule Content 

• Total Structure Weight: 36.17 kDa 
• Atom Count: 3,032 
• Modeled Residue Count: 322 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP8*	A, B	161	Rotavirus A	Mutation(s): 0
UniProt
Find proteins for Q8JNB4 (Rotavirus A (strain RVA/Cow/United States/WC3/1981/G6P7[5])) Explore Q8JNB4  Go to UniProtKB:  Q8JNB4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.753	α = 90
b = 102.364	β = 90
c = 137.722	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-29 
Deposition Author(s): Duan, Z., Sun, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21934005

Revision History  

• Version 1.0: 2021-12-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description