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- PDB-3upv: TPR2B-domain:pHsp70-complex of yeast Sti1 -

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Basic information

Entry
Database: PDB / ID: 3upv
TitleTPR2B-domain:pHsp70-complex of yeast Sti1
Components
  • Heat shock protein SSA4Heat shock response
  • Heat shock protein STI1Heat shock response
KeywordsPEPTIDE BINDING PROTEIN / TPR-fold / Adaptor protein for Hsp70 and Hsp90 / C-terminal part of Hsp70
Function / homology
Function and homology information


RND1 GTPase cycle / Clathrin-mediated endocytosis / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ATPase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane, translocation / misfolded protein binding / protein targeting to mitochondrion / Protein methylation ...RND1 GTPase cycle / Clathrin-mediated endocytosis / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ATPase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane, translocation / misfolded protein binding / protein targeting to mitochondrion / Protein methylation / chaperone cofactor-dependent protein refolding / response to unfolded protein / cellular response to unfolded protein / protein folding chaperone / vesicle-mediated transport / Hsp70 protein binding / heat shock protein binding / Neutrophil degranulation / Hsp90 protein binding / protein localization / unfolded protein binding / protein folding / cellular response to heat / protein refolding / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / 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. ...STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / 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 / Tetratricopeptide repeat / 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 STI1 / Heat shock protein SSA4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchmid, A.B. / Lagleder, S. / Graewert, M.A. / Roehl, A. / Hagn, F. / Wandinger, S.K. / Cox, M.B. / Demmer, O. / Richter, K. / Groll, M. / Kessler, H.
CitationJournal: Embo J. / Year: 2012
Title: The architecture of functional modules in the Hsp90 co-chaperone Sti1/Hop.
Authors: Schmid, A.B. / Lagleder, S. / Grawert, M.A. / Rohl, A. / Hagn, F. / Wandinger, S.K. / Cox, M.B. / Demmer, O. / Richter, K. / Groll, M. / Kessler, H. / Buchner, J.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein STI1
B: Heat shock protein SSA4


Theoretical massNumber of molelcules
Total (without water)14,9592
Polymers14,9592
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-1 kcal/mol
Surface area7020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.630, 38.630, 176.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Heat shock protein STI1 / Heat shock response


Mass: 14170.914 Da / Num. of mol.: 1 / Fragment: TPR repeats 7-9, residues 395-518
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: STI1, YOR027W, OR26.17 / Production host: Escherichia coli (E. coli) / References: UniProt: P15705
#2: Protein/peptide Heat shock protein SSA4 / Heat shock response


Mass: 787.811 Da / Num. of mol.: 1 / Fragment: UNP residues 636-642 / Source method: obtained synthetically / Details: Heptapeptide; C-terminus of Hsp70 from yeast / Source: (synth.) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P22202
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M LiCl, 2.2 M Ammoniumsulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2009
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→10 Å / Num. all: 18603 / Num. obs: 17394 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.03
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.1 / % possible all: 93.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ELR

1elr


Resolution: 1.6→9.86 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.795 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25443 870 5 %RANDOM
Rwork0.18259 ---
all0.191 17394 --
obs0.18618 16524 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.168 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→9.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 0 143 1181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221053
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.961417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7495130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45724.42352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25815190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.922159
X-RAY DIFFRACTIONr_chiral_restr0.1220.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021800
X-RAY DIFFRACTIONr_mcbond_it1.8941.5661
X-RAY DIFFRACTIONr_mcangle_it2.62821051
X-RAY DIFFRACTIONr_scbond_it4.8213392
X-RAY DIFFRACTIONr_scangle_it6.8154.5366
X-RAY DIFFRACTIONr_rigid_bond_restr2.63931053
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 60 -
Rwork0.227 1146 -
obs--100 %
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)
110.4998-1.88583.4160.0218-0.74196.25790.02170.67870.0325-0.0562-0.2325-0.1487-0.0335-0.08930.21080.07560.0619-0.01270.13210.00880.0869-1.5842-16.4108-4.7858
28.4876-0.50312.6479-0.12820.82134.73670.07070.0927-0.4061-0.0345-0.05260.08650.05110.1471-0.01820.07720.0675-0.02780.0835-0.03040.03854.261-19.84171.2556
35.492-0.20980.30810.49261.04441.05280.00780.05360.0827-0.05670.1176-0.15230.06140.2142-0.12540.09560.04320.04350.0838-0.00490.042212.4958-17.0176.261
42.5623-0.66472.0150.5207-1.03062.4493-0.01640.1825-0.0026-0.1163-0.0331-0.00680.0110.07620.04960.09270.0079-0.01050.06670.00710.02273.3258-10.64732.7074
55.23080.5599-0.91660.3873-1.50492.59890.09320.1579-0.0552-0.01570.04610.0639-0.1454-0.1656-0.13930.0960.04930.00040.08860.02450.0341-5.3847-8.70831.1603
61.62530.06170.43970.58430.10241.0660.01480.0382-0.0027-0.01590.0425-0.0331-0.0320.0282-0.05730.03010.0075-0.00770.04310.01380.04355.0598-12.179213.3202
74.12290.94531.33051.63260.461.4349-0.11820.09660.21430.05330.06780.0683-0.1201-0.10350.05040.03970.02930.01080.03880.01680.0544-1.0651-7.849816.0253
82.3537-2.2570.7044-1.5762-1.75994.66390.0314-0.094-0.2442-0.19170.32870.193-0.0523-1.0721-0.36020.00640.0018-0.02220.20310.0750.1007-10.4992-13.175413.6696
94.04571.31673.42010.7716-1.15093.6629-0.1050.1393-0.0522-0.05380.25450.0914-0.0945-0.0828-0.14950.034-0.00670.00360.04290.00920.0666-4.2641-18.75517.0598
101.03910.0563-0.23191.51630.66931.66330.1548-0.0290.02740.0939-0.1327-0.0404-0.11990.0225-0.02210.0564-0.0115-0.00390.02550.00170.05493.2579-11.927426.8726
113.83040.5466-1.825511.9415-0.8357-0.3463-0.1322-0.05430.08770.43490.21670.5622-0.0240.0292-0.08450.0685-0.00250.03050.01220.00140.0869-5.8576-15.951828.0025
1211.34238.26862.15775.67642.24320.87870.0742-0.05230.12730.1298-0.09530.13290.0548-0.34870.02120.022-0.01650.01240.0970.02370.0971-8.93-22.856925.1661
138.01582.97311.39721.1974-1.15281.1380.04430.1568-0.0097-0.14140.18260.10170.2893-0.1145-0.22690.0586-0.0438-0.00030.0405-0.02450.1053-7.8598-27.337421.1133
140.17850.9059-0.32684.49452.54473.93830.0459-0.051-0.04530.2783-0.1427-0.02640.21130.11540.09680.0397-0.0019-0.01350.04080.00780.07661.8421-23.9629.4449
153.74190.3487-1.752615.66211.35660.01850.44230.0289-0.03580.7906-0.4688-0.4594-0.0143-0.12670.02650.1495-0.0968-0.04730.06790.02170.0185.5228-15.563635.5357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A259 - 264
2X-RAY DIFFRACTION2A265 - 270
3X-RAY DIFFRACTION3A271 - 282
4X-RAY DIFFRACTION4A283 - 289
5X-RAY DIFFRACTION5A290 - 294
6X-RAY DIFFRACTION6A295 - 313
7X-RAY DIFFRACTION7A314 - 323
8X-RAY DIFFRACTION8A324 - 328
9X-RAY DIFFRACTION9A329 - 333
10X-RAY DIFFRACTION10A334 - 350
11X-RAY DIFFRACTION11A351 - 356
12X-RAY DIFFRACTION12A357 - 361
13X-RAY DIFFRACTION13A362 - 369
14X-RAY DIFFRACTION14A370 - 377
15X-RAY DIFFRACTION15A378 - 383

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