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- PDB-6olx: Hsp90-alpha S52A bound to PU-11-trans -

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Basic information

Entry
Database: PDB / ID: 6olx
TitleHsp90-alpha S52A bound to PU-11-trans
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE/CHAPERONE INHIBITOR / Hsp90 / Chaperone / Cytosol / Cancer / Inhibitor / CHAPERONE-CHAPERONE INHIBITOR complex
Function / homology
Function and homology information


sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity ...sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / protein unfolding / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / : / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of defense response to virus by host / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Recruitment of NuMA to mitotic centrosomes / response to salt stress / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / lysosomal lumen / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / Aggrephagy / positive regulation of protein import into nucleus / Chaperone Mediated Autophagy / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / Regulation of PLK1 Activity at G2/M Transition / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding
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-KFY / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43760580022 Å
AuthorsGewirth, D.T. / Huck, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA186866 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA095130 United States
CitationJournal: Proteins / Year: 2019
Title: Structures of Hsp90 alpha and Hsp90 beta bound to a purine-scaffold inhibitor reveal an exploitable residue for drug selectivity.
Authors: Huck, J.D. / Que, N.L.S. / Sharma, S. / Taldone, T. / Chiosis, G. / Gewirth, D.T.
History
DepositionApr 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1272
Polymers28,7571
Non-polymers3691
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.787, 91.384, 98.13
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / ...Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 28757.145 Da / Num. of mol.: 1 / Mutation: S52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P07900
#2: Chemical ChemComp-KFY / 9-[(2E)-but-2-en-1-yl]-8-[(3,4,5-trimethoxyphenyl)methyl]-9H-purin-6-amine


Mass: 369.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Na Cacodylate pH 6.5 160 mM MgCl2 6% PEG 2000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4376→66.876 Å / Num. obs: 54417 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 19.8779218561 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Net I/σ(I): 20
Reflection shellResolution: 1.4376→1.462 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2712 / CC1/2: 0.895 / Rpim(I) all: 0.229 / Rrim(I) all: 0.575 / % possible all: 100

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Processing

Software
NameVersionClassification
phenix.refine1.9_1692refinement
PHENIX1.9_1692refinement
autoPROCdata scaling
PHENIX1.9_1692phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43760580022→33.4380308421 Å / SU ML: 0.133238348605 / Cross valid method: FREE R-VALUE / σ(F): 1.38115573533 / Phase error: 17.5835261629
RfactorNum. reflection% reflection
Rfree0.18089920401 2685 4.93475464069 %
Rwork0.163027587293 51725 -
obs0.163890993175 54410 99.2159008023 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.7381574289 Å2
Refinement stepCycle: LAST / Resolution: 1.43760580022→33.4380308421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 27 350 1992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006569216917151708
X-RAY DIFFRACTIONf_angle_d1.097656252222312
X-RAY DIFFRACTIONf_chiral_restr0.0418082988854263
X-RAY DIFFRACTIONf_plane_restr0.00430157119512294
X-RAY DIFFRACTIONf_dihedral_angle_d12.9742169053632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4376-1.46370.2981355051111450.2335384264612703X-RAY DIFFRACTION99.9648999649
1.4637-1.49190.2124399217221300.2122913063012714X-RAY DIFFRACTION99.894625922
1.4919-1.52240.2283953986541400.2022030012752720X-RAY DIFFRACTION99.9650471863
1.5224-1.55550.2269132802281250.1899592407322727X-RAY DIFFRACTION99.9649491763
1.5555-1.59160.2077887697081200.1863235439072748X-RAY DIFFRACTION100
1.5916-1.63140.202681426821570.1810129331572702X-RAY DIFFRACTION100
1.6314-1.67550.2092885695591600.1859197218432688X-RAY DIFFRACTION100
1.6755-1.72490.1836312171451340.1789983320252732X-RAY DIFFRACTION100
1.7249-1.78050.2052297276681420.1731504566482705X-RAY DIFFRACTION100
1.7805-1.84420.2043917845251490.1719383125652715X-RAY DIFFRACTION100
1.8442-1.9180.1830401944531380.1738929939892767X-RAY DIFFRACTION100
1.918-2.00530.1857195333041490.1708435093882696X-RAY DIFFRACTION99.9648629656
2.0053-2.1110.1665257033261560.1632706376622731X-RAY DIFFRACTION99.9653739612
2.111-2.24320.1767994951011540.1557399741992740X-RAY DIFFRACTION100
2.2432-2.41640.1772775938141480.1631436031562751X-RAY DIFFRACTION99.8966230186
2.4164-2.65940.1873004785361340.1719085863762764X-RAY DIFFRACTION99.9655053467
2.6594-3.0440.2010058651551360.1686519635092790X-RAY DIFFRACTION99.8634812287
3.044-3.83430.1879559665251310.1518941947892511X-RAY DIFFRACTION89.8639455782
3.8343-33.44710.1392593802841370.1419672073842821X-RAY DIFFRACTION96.257728604

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