5LYP

Crystal structure of the Tpr Domain of Sgt2.

• PDB DOI: https://doi.org/10.2210/pdb5LYP/pdb

• Classification: CHAPERONE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-28 Released: 2017-10-25 
• Deposition Author(s): Krysztofinska, E.M., Morgan, R.M.L., Thapaliya, A., Evans, N.J., Murray, J.W., Martinez-Lumbreras, S., Isaacson, R.L.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.218 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Structure and Interactions of the TPR Domain of Sgt2 with Yeast Chaperones and Ybr137wp.

Krysztofinska, E.M., Evans, N.J., Thapaliya, A., Murray, J.W., Morgan, R.M.L., Martinez-Lumbreras, S., Isaacson, R.L.

(2017) Front Mol Biosci 4: 68-68

• PubMed: 29075633 
• DOI: https://doi.org/10.3389/fmolb.2017.00068
• Primary Citation of Related Structures:  
  5LYN, 5LYP


• PubMed Abstract: 
  

  Small glutamine-rich tetratricopeptide repeat-containing protein 2 (Sgt2) is a multi-module co-chaperone involved in several protein quality control pathways. The TPR domain of Sgt2 and several other proteins, including SGTA, Hop, and CHIP, is a highly conserved motif known to form transient complexes with molecular chaperones such as Hsp70 and Hsp90. In this work, we present the first high resolution crystal structures of Sgt2_TPR alone and in complex with a C-terminal peptide PTVEEVD from heat shock protein, Ssa1. Using nuclear magnetic resonance spectroscopy and isothermal titration calorimetry, we demonstrate that Sgt2_TPR interacts with peptides corresponding to the C-termini of Ssa1, Hsc82, and Ybr137wp with similar binding modes and affinities.

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Organizational Affiliation: 

Department of Chemistry, King's College London, London, United Kingdom.

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: 15.72 kDa 
• Atom Count: 1,157 
• Modelled Residue Count: 137 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small glutamine-rich tetratricopeptide repeat-containing protein 2	A	140	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SGT2, YOR007C, UNF346
UniProt
Find proteins for Q12118 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12118  Go to UniProtKB:  Q12118

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BO4	B [auth A]	BORATE ION B H4 O4 KCFLOKKYWBPKFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.218 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.861	α = 90
b = 50.76	β = 90
c = 67.116	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Krysztofinska, E.M., Morgan, R.M.L., Thapaliya, A., Evans, N.J., Murray, J.W., Martinez-Lumbreras, S., Isaacson, R.L.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/L006952/1

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description