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- PDB-3uq3: TPR2AB-domain:pHSP90-complex of yeast Sti1 -

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Basic information

Entry
Database: PDB / ID: 3uq3
TitleTPR2AB-domain:pHSP90-complex of yeast Sti1
Components
  • Heat shock protein
  • Heat shock protein STI1
KeywordsCHAPERONE / Hsp90 / peptide binding
Function / homology
Function and homology information


RND1 GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ATPase inhibitor activity / protein targeting to mitochondrion / Hsp70 protein binding / Hsp90 protein binding / intracellular protein localization / protein folding / mRNA binding / 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 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. ...STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein STI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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. ...Schmid, 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. / Buchner, J.
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 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _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
C: Heat shock protein


Theoretical massNumber of molelcules
Total (without water)30,5883
Polymers30,5883
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-3 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.191, 62.897, 66.842
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe AU contains one biological assembly

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Components

#1: Protein Heat shock protein STI1


Mass: 29344.836 Da / Num. of mol.: 1 / Fragment: TPR repeats 4-9, residues 262-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: STI1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Codon Plus / References: UniProt: P15705
#2: Protein/peptide Heat shock protein


Mass: 621.657 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in yeast - C-terminus of HSP90.
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.2 M TMAO, 0.1 M Tris, 20% PEG 2000 MME, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 14, 2011
RadiationMonochromator: graphite monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 18105 / Num. obs: 17924 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.26
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PROTEUM2data collection
PHASERphasing
REFMAC5.5.0109refinement
PROTEUM2data reduction
PROTEUM2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ELR

1elr


Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 29.877 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27854 545 5 %RANDOM
Rwork0.21719 ---
obs0.22027 17480 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.607 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å21.2 Å2
2---2.25 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 0 52 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022165
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.9592908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7295263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90524.779113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22615403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0471515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021657
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9151.51325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60822102
X-RAY DIFFRACTIONr_scbond_it3.2423842
X-RAY DIFFRACTIONr_scangle_it5.1384.5808
X-RAY DIFFRACTIONr_rigid_bond_restr1.28132165
X-RAY DIFFRACTIONr_sphericity_free45.899515
X-RAY DIFFRACTIONr_sphericity_bonded7.63352169
LS refinement shellResolution: 2.6→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 37 -
Rwork0.286 683 -
obs--97.17 %
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)
110.1030.4675-4.5943.7267-0.609311.15430.03860.06190.2843-0.3794-0.23190.1227-0.2658-0.38780.19330.07750.0721-0.01560.09770.02070.07432.38692.0981-8.1321
24.4818-1.3185-1.74395.8117-0.86363.4462-0.0442-0.22240.06420.31350.0427-0.20050.0833-0.3060.00160.0301-0.0172-0.01720.09570.02060.06375.88090.09670.6519
39.0358-4.0987-0.29783.20934.396413.80020.2490.06640.8835-0.2437-0.0948-0.5679-0.4581-0.1498-0.15410.04540.03860.02860.14580.1440.539417.5816-2.9638-9.9595
44.6799-0.4734-6.23766.6111-1.43949.5272-0.1114-0.4170.15590.73990.0927-0.2801-0.09090.37450.01870.12610.0664-0.06120.2190.01450.185212.6261-8.03136.0967
52.0819-2.61930.9324.59540.37132.2512-0.1266-0.2494-0.04370.57350.2485-0.05110.4023-0.2058-0.12190.140.0078-0.050.13650.04420.098411.8267-13.2517-0.5181
66.5025-1.2967-0.11696.0495-0.70884.0547-0.0167-0.08390.072-0.1405-0.1705-0.51590.30040.51370.18720.04020.0559-0.02770.0845-0.01840.193520.4227-16.4387-3.8289
79.1498-2.3519-3.1160.85761.10255.9647-0.14290.4998-0.3275-0.1154-0.1774-0.1140.9554-0.08950.32030.47720.0920.10510.1153-0.01560.340218.7883-24.2123-9.2837
85.6761-3.6539-1.74189.36362.03893.67570.0953-0.19770.2254-0.1420.1167-0.5032-0.38880.4111-0.2120.17450.0328-0.00290.15560.02440.122545.1834-27.4346-16.2747
98.61264.2623-3.600421.01844.19825.5084-0.1653-0.43390.20670.02640.3947-1.2914-0.24630.7877-0.22930.20690.0788-0.1160.2639-0.00980.263452.6238-44.1916-13.4876
103.4428-2.17731.3646.58541.1771.5998-0.0162-0.15210.0930.178-0.12460.20660.0697-0.02840.14070.03840.02330.0180.0889-0.00780.01943.5814-38.8512-18.6672
114.73150.16760.30245.74470.24711.6997-0.15830.01620.1138-0.59380.26040.36780.2599-0.3142-0.10210.1916-0.0423-0.02180.15170.01030.113839.8793-46.3054-27.3068
125.44140.5836-1.79698.6108-1.96295.8684-0.05520.4670.0236-0.57860.1414-0.0038-0.041-0.1596-0.08620.2422-0.08210.01290.1523-0.06860.107943.6422-51.0123-37.4063
1332.93944.0491-3.21428.2937-7.79075.9741-0.10260.7893-1.1415-0.662-0.23010.42170.3566-1.09960.33260.4412-0.076-0.03140.3967-0.07350.214543.1059-61.9242-36.0795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A258 - 283
2X-RAY DIFFRACTION2A284 - 304
3X-RAY DIFFRACTION3A305 - 312
4X-RAY DIFFRACTION4A313 - 332
5X-RAY DIFFRACTION5A333 - 343
6X-RAY DIFFRACTION6A344 - 366
7X-RAY DIFFRACTION7A367 - 384
8X-RAY DIFFRACTION8A385 - 401
9X-RAY DIFFRACTION9A402 - 414
10X-RAY DIFFRACTION10A415 - 443
11X-RAY DIFFRACTION11A444 - 477
12X-RAY DIFFRACTION12A478 - 509
13X-RAY DIFFRACTION13A510 - 515

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