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- PDB-5lyn: Structure of the Tpr Domain of Sgt2 in complex with yeast Ssa1 pe... -

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Basic information

Entry
Database: PDB / ID: 5lyn
TitleStructure of the Tpr Domain of Sgt2 in complex with yeast Ssa1 peptide fragment
Components
  • PRO-THR-VAL-GLU-GLU-VAL-ASP
  • Small glutamine-rich tetratricopeptide repeat-containing protein 2
KeywordsCHAPERONE
Function / homology
Function and homology information


: / Regulation of HSF1-mediated heat shock response / TRC complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondria-associated ubiquitin-dependent protein catabolic process / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / fungal-type cell wall / clathrin coat disassembly / response to oxygen levels / post-translational protein targeting to endoplasmic reticulum membrane ...: / Regulation of HSF1-mediated heat shock response / TRC complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondria-associated ubiquitin-dependent protein catabolic process / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / fungal-type cell wall / clathrin coat disassembly / response to oxygen levels / post-translational protein targeting to endoplasmic reticulum membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to mitochondrion / fungal-type vacuole membrane / stress granule disassembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / heat shock protein binding / transcription repressor complex / ATP-dependent protein folding chaperone / protein polyubiquitination / protein import into nucleus / unfolded protein binding / protein folding / cytoplasmic translation / response to heat / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / tRNA binding / molecular adaptor activity / negative regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular region / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily ...SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / ATPase, nucleotide binding domain / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein SSA1 / Small glutamine-rich tetratricopeptide repeat-containing protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKrysztofinska, E.M. / Evans, N.J. / Thapaliya, A. / Murray, J.W. / Morgan, R.M.L. / Martinez-Lumbreras, S. / Isaacson, R.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L006952/1 United Kingdom
CitationJournal: Front Mol Biosci / Year: 2017
Title: Structure and Interactions of the TPR Domain of Sgt2 with Yeast Chaperones and Ybr137wp.
Authors: Krysztofinska, E.M. / Evans, N.J. / Thapaliya, A. / Murray, J.W. / Morgan, R.M.L. / Martinez-Lumbreras, S. / Isaacson, R.L.
History
DepositionSep 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small glutamine-rich tetratricopeptide repeat-containing protein 2
B: Small glutamine-rich tetratricopeptide repeat-containing protein 2
C: PRO-THR-VAL-GLU-GLU-VAL-ASP
D: PRO-THR-VAL-GLU-GLU-VAL-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,80813
Polymers31,2194
Non-polymers5899
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-202 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.490, 61.090, 55.250
Angle α, β, γ (deg.)90.000, 108.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resseq 93:133)
21(chain B and resseq 93:133)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 93 - 133 / Label seq-ID: 1 - 41

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resseq 93:133)AA
2(chain B and resseq 93:133)BB

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Components

#1: Protein Small glutamine-rich tetratricopeptide repeat-containing protein 2 / SGT/UBP / Viral protein U-binding protein


Mass: 14821.651 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SGT2, YOR007C, UNF346 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12118
#2: Protein/peptide PRO-THR-VAL-GLU-GLU-VAL-ASP


Mass: 787.811 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10591*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293.15 K / Method: batch mode / pH: 7.2 / Details: 0.2 M Zinc Acetate, 30% PEG 3350 / PH range: 6.6-8.0

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Data collection

DiffractionMean temperature: 298.15 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→33.59 Å / Num. obs: 19295 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Net I/σ(I): 16.4 / Num. measured all: 126863 / Scaling rejects: 59
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.056.40.3920.913198
8.94-33.595.80.0560.995196.7

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VYI

2vyi


Resolution: 2→33.586 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.37
RfactorNum. reflection% reflection
Rfree0.2025 928 4.81 %
Rwork0.1576 --
obs0.1598 19279 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.21 Å2 / Biso mean: 30.7791 Å2 / Biso min: 11.1 Å2
Refinement stepCycle: final / Resolution: 2→33.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 9 148 2340
Biso mean--50.77 34.38 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062213
X-RAY DIFFRACTIONf_angle_d0.682971
X-RAY DIFFRACTIONf_chiral_restr0.041319
X-RAY DIFFRACTIONf_plane_restr0.005389
X-RAY DIFFRACTIONf_dihedral_angle_d15.8981384
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A390X-RAY DIFFRACTION0.816TORSIONAL
12B390X-RAY DIFFRACTION0.816TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.10540.24761110.18452617272898
2.1054-2.23730.21531540.16042570272499
2.2373-2.410.20081190.16112616273599
2.41-2.65250.23651530.1692599275299
2.6525-3.03610.2061230.17212644276799
3.0361-3.82430.20211280.16092629275799
3.8243-33.59050.17771400.13752676281699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0429-0.50010.62720.3438-0.66261.4787-0.07820.3598-0.0578-0.12080.0681-0.1575-0.50340.6587-0.03820.2178-0.09820.01920.3905-0.04580.21151.145412.7452-7.7343
20.42870.36930.01190.0868-0.07881.26940.01620.0907-0.1326-0.13380.1414-0.174-0.06610.32930.00040.14910.0123-0.00140.2025-0.02870.1533-8.7036.824-8.5038
30.4293-0.2081-0.11140.6686-0.0220.89010.04120.00570.1077-0.0145-0.00530.0277-0.0319-0.0702-00.1684-0.0075-0.00130.1307-0.0070.1643-17.03929.149-22.269
40.17520.0198-0.01160.22020.0070.52620.13280.8404-0.0853-0.25910.2125-0.24610.074-0.14240.00760.314-0.0196-0.00810.25530.0050.2722-19.68340.1949-32.5503
50.3543-0.14890.07250.43910.03860.0824-0.1168-0.1809-0.24850.23780.0560.28750.2737-0.4352-0.0750.2348-0.06140.02740.2498-0.01360.201-6.96633.7912-49.5513
60.1545-0.18290.39980.74090.46851.9436-0.04510.0610.0223-0.02970.0466-0.01480.0680.0576-0.00010.1441-0.00290.00810.13850.00820.14195.529311.4478-44.3841
71.7508-0.1748-1.02080.08140.23480.80860.4112-0.37810.37370.1875-0.0452-0.1449-0.24940.05480.09140.1761-0.0239-0.02120.22040.00020.18174.846619.9426-29.3257
80.02250.0327-0.00140.1546-0.07160.0171-0.02360.0668-0.02050.09280.1424-0.21150.2125-0.1454-0.00010.1703-0.0099-0.06210.21290.01380.342314.580217.7372-24.9031
90.01520.01830.0217-0.0196-0.00490.00230.3234-0.0510.1256-0.25260.05880.1615-0.0427-0.1982-0.00020.48350.1061-0.01030.49750.02550.44354.91486.2816-34.8933
100.02370.01370.01590.0072-0.02280.03290.18330.3908-0.0335-0.2096-0.1522-0.2846-0.41-0.0686-0.00010.48870.025-0.06290.6665-0.06150.4554-7.31752.5042-20.3019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 93 through 114 )A93 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 151 )A115 - 151
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 203 )A152 - 203
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 225 )A204 - 225
5X-RAY DIFFRACTION5chain 'B' and (resid 93 through 114 )B93 - 114
6X-RAY DIFFRACTION6chain 'B' and (resid 115 through 185 )B115 - 185
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 205 )B186 - 205
8X-RAY DIFFRACTION8chain 'B' and (resid 206 through 225 )B206 - 225
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 7 )C1 - 7
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 7 )D1 - 7

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