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- PDB-2llv: Solution structure of the yeast Sti1 DP1 domain -

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Basic information

Entry
Database: PDB / ID: 2llv
TitleSolution structure of the yeast Sti1 DP1 domain
ComponentsHeat shock protein STI1
KeywordsCHAPERONE / DP domain / Alpha helix
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 / protein localization / protein folding / mRNA binding / cytoplasm
Similarity search - Function
434 Repressor (Amino-terminal Domain) - #100 / STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 434 Repressor (Amino-terminal Domain) / Tetratricopeptide repeat ...434 Repressor (Amino-terminal Domain) - #100 / STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 434 Repressor (Amino-terminal Domain) / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein STI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
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 17, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein STI1


Theoretical massNumber of molelcules
Total (without water)7,9351
Polymers7,9351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Heat shock protein STI1


Mass: 7935.260 Da / Num. of mol.: 1 / Fragment: STI1 1 domain residues 127-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: OR26.17, STI1, YOR027W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P15705

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aromatic
1422D 1H-1H NOESY
1513D HNCO
1613D HN(CA)CO
1713D HN(CO)CA
1813D HNCA
1913D CBCA(CO)NH
11013D HN(CA)CB
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY
11313D C(CO)NH
11413D HNHA
11513D HNHB
11613D 1H-13C NOESY
11733D 1H-15N NOESY
11813D CNH NOESY
11913D CCH NOESY
12033D NNH NOESY
12112D (HB)CB(CGCD)HD
12212D (HB)CB(CGCDCE)HE
12332D 1H-15N HSQC-IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-3 mM [U-99% 13C; U-99% 15N] DP1, 50 mM potassium chloride, 50 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM DP1, 50 mM potassium chloride, 50 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM [U-99% 15N] DP1, 50 mM potassium chloride, 50 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDP1-1[U-99% 13C; U-99% 15N]0.5-31
50 mMpotassium chloride-21
50 mMpotassium phosphate-31
0.2 w/vsodium azide-41
0.5 mMDP1-52
50 mMpotassium chloride-62
50 mMpotassium phosphate-72
0.2 w/vsodium azide-82
0.5 mMDP1-9[U-99% 15N]3
50 mMpotassium chloride-103
50 mMpotassium phosphate-113
0.2 w/vsodium azide-123
Sample conditionsIonic strength: 0.35 / pH: 7.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
ProcheckNMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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