4JRU | pdb_00004jru

Structure of haze forming proteins in white wines: Vitis vinifera thaumatin-like proteins

• PDB DOI: https://doi.org/10.2210/pdb4JRU/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Vitis vinifera
• Mutation(s): No 


• Deposited: 2013-03-22 Released: 2014-04-02 
• Deposition Author(s): Marangon, M., Menz, R.I., Waters, E.J., Van Sluyter, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Structure of Haze Forming Proteins in White Wines: Vitis vinifera Thaumatin-Like Proteins.

Marangon, M., Van Sluyter, S.C., Waters, E.J., Menz, R.I.

(2014) PLoS One 9: e113757-e113757

• PubMed: 25463627 
• DOI: https://doi.org/10.1371/journal.pone.0113757
• Primary Citation Related Structures: 
  4JRU, 4L5H, 4MBT


• PubMed Abstract: 
  

  Grape thaumatin-like proteins (TLPs) play roles in plant-pathogen interactions and can cause protein haze in white wine unless removed prior to bottling. Different isoforms of TLPs have different hazing potential and aggregation behavior. Here we present the elucidation of the molecular structures of three grape TLPs that display different hazing potential. The three TLPs have very similar structures despite belonging to two different classes (F2/4JRU is a thaumatin-like protein while I/4L5H and H2/4MBT are VVTL1), and having different unfolding temperatures (56 vs. 62°C), with protein F2/4JRU being heat unstable and forming haze, while I/4L5H does not. These differences in properties are attributable to the conformation of a single loop and the amino acid composition of its flanking regions.

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Organizational Affiliation: 
• The Australian Wine Research Institute, Adelaide, South Australia, Australia.
The Australian Wine Research Institute, Adelaide, South Australia, Australia; School of Botany, University of Melbourne, Victoria, Australia.
School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 21.54 kDa 
• Atom Count: 1,763 
• Modeled Residue Count: 201 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thaumatin-like protein	A	201	Vitis vinifera	Mutation(s): 0
UniProt
Find proteins for F6HUG9 (Vitis vinifera) Explore F6HUG9  Go to UniProtKB:  F6HUG9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.801	α = 90
b = 70.168	β = 90
c = 74.895	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Marangon, M., Menz, R.I., Waters, E.J., Van Sluyter, S.C.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary