6H9Y | pdb_00006h9y

Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens

• PDB DOI: https://doi.org/10.2210/pdb6H9Y/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human rotavirus A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-06 Released: 2019-06-12 
• Deposition Author(s): Ciges-Tomas, J.R., Gozalbo-Rovira, R., Vila-Vicent, S., Buesa, J., Santiso-Bellon, C., Monedero, V., Yebra, M.J., Rodriguez-Diaz, J., Marina, A.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens.

Gozalbo-Rovira, R., Ciges-Tomas, J.R., Vila-Vicent, S., Buesa, J., Santiso-Bellon, C., Monedero, V., Yebra, M.J., Marina, A., Rodriguez-Diaz, J.

(2019) PLoS Pathog 15: e1007865-e1007865

• PubMed: 31226167 
• DOI: https://doi.org/10.1371/journal.ppat.1007865
• Primary Citation Related Structures: 
  6H9W, 6H9Y, 6H9Z, 6HA0


• PubMed Abstract: 
  

  Rotavirus is the leading agent causing acute gastroenteritis in young children, with the P[8] genotype accounting for more than 80% of infections in humans. The molecular bases for binding of the VP8* domain from P[8] VP4 spike protein to its cellular receptor, the secretory H type-1 antigen (Fuc-α1,2-Gal-β1,3-GlcNAc; H1), and to its precursor lacto-N-biose (Gal-β1,3-GlcNAc; LNB) have been determined. The resolution of P[8] VP8* crystal structures in complex with H1 antigen and LNB and site-directed mutagenesis experiments revealed that both glycans bind to the P[8] VP8* protein through a binding pocket shared with other members of the P[II] genogroup (i.e.: P[4], P[6] and P[19]). Our results show that the L-fucose moiety from H1 only displays indirect contacts with P[8] VP8*. However, the induced conformational changes in the LNB moiety increase the ligand affinity by two-fold, as measured by surface plasmon resonance (SPR), providing a molecular explanation for the different susceptibility to rotavirus infection between secretor and non-secretor individuals. The unexpected interaction of P[8] VP8* with LNB, a building block of type-1 human milk oligosaccharides, resulted in inhibition of rotavirus infection, highlighting the role and possible application of this disaccharide as an antiviral. While key amino acids in the H1/LNB binding pocket were highly conserved in members of the P[II] genogroup, differences were found in ligand affinities among distinct P[8] genetic lineages. The variation in affinities were explained by subtle structural differences induced by amino acid changes in the vicinity of the binding pocket, providing a fine-tuning mechanism for glycan binding in P[8] rotavirus.

---

Organizational Affiliation: 
• Departament of Microbiology, Faculty of Medicine, University of Valencia, Valencia, Spain.
Department of Genomic and Proteomic, Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Spain.

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)

Macromolecule Content 

• Total Structure Weight: 37.69 kDa 
• Atom Count: 3,204 
• Modeled Residue Count: 322 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP4	A, B	162	Human rotavirus A	Mutation(s): 0  Gene Names: VP4
UniProt
Find proteins for Q0PRF2 (Human rotavirus A) Explore Q0PRF2  Go to UniProtKB:  Q0PRF2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan: G00056MO GlyCosmos: G00056MO GlyGen: G00056MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	D [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.988	α = 90
b = 54.725	β = 97.92
c = 67.433	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Ciges-Tomas, J.R., Gozalbo-Rovira, R., Vila-Vicent, S., Buesa, J., Santiso-Bellon, C., Monedero, V., Yebra, M.J., Rodriguez-Diaz, J., Marina, A.

---

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-78571-P

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary