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- PDB-1zw9: Yeast HSP82 in complex with the Novel HSP90 Inhibitor 8-(6-Bromo-... -

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Basic information

Entry
Database: PDB / ID: 1zw9
TitleYeast HSP82 in complex with the Novel HSP90 Inhibitor 8-(6-Bromo-benzo[1,3]dioxol-5-ylsulfanyl)-9-(3-isopropylamino-propyl)-adenine
ComponentsHSP82
KeywordsCHAPERONE / HSP82 / HSP90 / GRP94 / HtpG / Ligand / Adenosine
Function / homology
Function and homology information


The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels ...The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / : / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H64 / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsImmormino, R.M. / Gewirth, D.T. / Chiosis, G.
CitationJournal: To be Published
Title: Inhibitory Ligands Adopt Different Conformations When Bound to Hsp90 or GRP94: Implications for Paralog-specific Drug Design
Authors: Immormino, R.M. / Gewirth, D.T. / Chiosis, G.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5102
Polymers27,0451
Non-polymers4651
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.760, 73.760, 110.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1221-

HOH

21A-1241-

HOH

31A-1252-

HOH

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Components

#1: Protein HSP82 / Heat shock protein Hsp90 heat inducible isoform / 82 kDa heat shock protein


Mass: 27044.770 Da / Num. of mol.: 1 / Fragment: N-terminal Domain of HSP82 (Residues 1-220)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HSP82 / Plasmid: pPET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P02829
#2: Chemical ChemComp-H64 / 8-(6-BROMO-BENZO[1,3]DIOXOL-5-YLSULFANYL)-9-(3-ISOPROPYLAMINO-PROPYL)-ADENINE


Mass: 465.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21BrN6O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 3 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.6
Details: PEG 3350 ,Ammonium dihydrogen phosphate , pH 4.6, Micro-batch, temperature 291K

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Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 18, 2005 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24557 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.55 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 16.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.56 % / Mean I/σ(I) obs: 5.35 / Num. unique all: 2444 / Rsym value: 0.39 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2108270.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2323 9.5 %RANDOM
Rwork0.204 ---
obs-24542 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.2878 Å2 / ksol: 0.366135 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å20 Å20 Å2
2---2.88 Å20 Å2
3---5.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 28 323 2082
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rwork0.263 173
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3HH064A.paramHH064A.top

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