3TAY

Crystal structure of porcine rotavirus CRW-8 VP8* in complex with N-glycolylneuraminic acid

• PDB DOI: https://doi.org/10.2210/pdb3TAY/pdb

• Classification: SUGAR BINDING PROTEIN, VIRAL PROTEIN
• Organism(s): Porcine rotavirus (serotype 3 / strain CRW-8)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-08-04 Released: 2012-10-17 
• Deposition Author(s): Yu, X., Blanchard, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.225 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.65 kDa 
• Atom Count: 3,105 
• Modelled Residue Count: 326 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP4	A, B	163	Porcine rotavirus (serotype 3 / strain CRW-8)	Mutation(s): 5
UniProt
Find proteins for P0C6Y8 (Rotavirus A (isolate RVA/Pig/Australia/CRW-8/1987/G3P9[7])) Explore P0C6Y8  Go to UniProtKB:  P0C6Y8

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN0	C [auth A], K [auth B]	methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid C12 H21 N O10 NFUCYHODBBSMAK-BLMTXZDNSA-N
EPE	H [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
BEN	I [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
MPD	F [auth A], G [auth A], L [auth B], M [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	J [auth A], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MN0	Binding MOAD:  3TAY	Kd: 4.20e+5 (nM) from 1 assay(s)
	PDBBind:  3TAY	Kd: 4.20e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.225 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.982	α = 90
b = 59.646	β = 90
c = 111.964	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Yu, X., Blanchard, H.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Structure summary