6HA0

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

• PDB DOI: https://doi.org/10.2210/pdb6HA0/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Rotavirus A
• Expression System: Escherichia coli
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.233 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

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: 37.63 kDa 
• Atom Count: 2,819 
• Modelled 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	Rotavirus A	Mutation(s): 0  Gene Names: VP4
UniProt
Find proteins for A0A0S0VKY7 (Rotavirus A) Explore A0A0S0VKY7  Go to UniProtKB:  A0A0S0VKY7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G40696TO GlyCosmos:  G40696TO GlyGen:  G40696TO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900049	C	H type 1 antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.233 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.739	α = 90
b = 54.641	β = 97.73
c = 67.944	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.

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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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary