7JHZ | pdb_00007jhz

Crystal structure of the carbohydrate-binding domain VP8* of human P[8] rotavirus strain BM13851 in complex with LNDFH I

• PDB DOI: https://doi.org/10.2210/pdb7JHZ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human rotavirus A
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-21 Released: 2021-07-28 
• Deposition Author(s): Xu, S., Stuckert, M.R., McGinnis, K.R., Jiang, X., Kennedy, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens.

Xu, S., McGinnis, K.R., Liu, Y., Huang, P., Tan, M., Stuckert, M.R., Burnside, R.E., Jacob, E.G., Ni, S., Jiang, X., Kennedy, M.A.

(2021) Proc Natl Acad Sci U S A 118

• PubMed: 34475219 
• DOI: https://doi.org/10.1073/pnas.2107963118
• Primary Citation Related Structures: 
  6UT9, 6VKX, 7JHZ, 7KHU, 7KI5


• PubMed Abstract: 
  

  Group A rotaviruses cause severe gastroenteritis in infants and young children worldwide, with P[II] genogroup rotaviruses (RVs) responsible for >90% of global cases. RVs have diverse host ranges in different human and animal populations determined by host histo-blood group antigen (HBGA) receptor polymorphism, but details governing diversity, host ranges, and species barriers remain elusive. In this study, crystal structures of complexes of the major P[II] genogroup P[4] and P[8] genotype RV VP8* receptor-binding domains together with Lewis epitope-containing LNDFH I glycans in combination with VP8* receptor-glycan ligand affinity measurements based on NMR titration experiments revealed the structural basis for RV genotype-specific switching between ββ and βα HBGA receptor-binding sites that determine RV host ranges. The data support the hypothesis that P[II] RV evolution progressed from animals to humans under the selection of type 1 HBGAs guided by stepwise host synthesis of type 1 ABH and Lewis HBGAs. The results help explain disease burden, species barriers, epidemiology, and limited efficacy of current RV vaccines in developing countries. The structural data has the potential to impact the design of future vaccine strategies against RV gastroenteritis.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056.
Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Tianjin 100730, China.
Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.
Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267.
Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229; [e-mail] [e-mail].
Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056; [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.23 kDa 
• Atom Count: 3,802 
• Modeled Residue Count: 449 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP4	A, B, C	160	Human rotavirus A	Mutation(s): 0  Gene Names: VP8
UniProt
Find proteins for H6WUJ8 (Human rotavirus A) Explore H6WUJ8  Go to UniProtKB:  H6WUJ8

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	D [auth F]	6		N/A
Glycosylation Resources
GlyTouCan: G09552LA GlyCosmos: G09552LA GlyGen: G09552LA

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	E	5		N/A
Glycosylation Resources
GlyTouCan: G10333YJ GlyCosmos: G10333YJ GlyGen: G10333YJ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B], G [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.192	α = 90
b = 63.39	β = 91.15
c = 72.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Xu, S., Stuckert, M.R., McGinnis, K.R., Jiang, X., Kennedy, M.A.

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2021-09-22
  Changes: Advisory, Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description