5LYN | pdb_00005lyn

Structure of the Tpr Domain of Sgt2 in complex with yeast Ssa1 peptide fragment

PDB DOI: https://doi.org/10.2210/pdb5LYN/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., Evans, N.J., Thapaliya, A., Murray, J.W., Morgan, R.M.L., Martinez-Lumbreras, S., Isaacson, R.L.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.203 (Depositor), 0.204 (DCC)
R-Value Work:
0.158 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fmolb.2017.00068
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 31.81 kDa
Atom Count: 2,340
Modeled Residue Count: 280
Deposited Residue Count: 280
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small glutamine-rich tetratricopeptide repeat-containing protein 2	A, B	133	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12118
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PRO-THR-VAL-GLU-GLU-VAL-ASP	C, D	7	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P10591 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10591 Go to UniProtKB: P10591
Entity Groups
UniProt Group	P10591
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203 (Depositor), 0.204 (DCC)
R-Value Work: 0.158 (Depositor), 0.159 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.49	α = 90
b = 61.09	β = 108.81
c = 55.25	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Martinez-Lumbreras, S.

Isaacson, R.L.

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

Revision History (Full details and data files)

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, Derived calculations, Refinement description