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- PDB-6n8y: Hsp90-beta bound to PU-11-trans -

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Basic information

Entry
Database: PDB / ID: 6n8y
TitleHsp90-beta bound to PU-11-trans
ComponentsHeat shock protein HSP 90-beta
Keywordschaperone/chaperone inhibitor / HSP90 / Inhibitor / Cancer / Cytosol / CHAPERONE / chaperone-chaperone inhibitor complex
Function / homology
Function and homology information


HSP90-CDC37 chaperone complex / receptor ligand inhibitor activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity ...HSP90-CDC37 chaperone complex / receptor ligand inhibitor activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity / protein folding chaperone complex / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / The NLRP3 inflammasome / : / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / cellular response to interleukin-4 / Purinergic signaling in leishmaniasis infection / axonal growth cone / DNA polymerase binding / supramolecular fiber organization / chaperone-mediated protein folding / heat shock protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / ESR-mediated signaling / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / peptide binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / placenta development / tau protein binding / kinase binding / Regulation of actin dynamics for phagocytic cup formation / histone deacetylase binding / Chaperone Mediated Autophagy / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / double-stranded RNA binding / unfolded protein binding / melanosome / protein folding / MHC class II protein complex binding / regulation of protein localization / cellular response to heat / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / protein dimerization activity / regulation of cell cycle / protein stabilization / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / negative regulation of apoptotic process / virion attachment to host cell / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / 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-KFY / Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55390799533 Å
AuthorsHuck, J.D. / Que, N.L.S. / Gewirth, D.T.
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
DepositionNov 30, 2018Deposition 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 1.4Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,3442
Polymers26,9741
Non-polymers3691
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.144, 90.959, 96.196
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-697-

HOH

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Components

#1: Protein Heat shock protein HSP 90-beta / HSP 90 / Heat shock 84 kDa / HSP84


Mass: 26974.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPCB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P08238
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES pH 6.5, MgCl2, PEG 2000 MME. Incubate with PU-11-trans prior to setup.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.42→28.96 Å / Num. obs: 53866 / % possible obs: 96.1 % / Redundancy: 7 % / Biso Wilson estimate: 21.7009285782 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.4
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1748 / CC1/2: 0.752 / % possible all: 64.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T0H

3t0h


Resolution: 1.55390799533→22.73975 Å / SU ML: 0.126301306084 / Cross valid method: FREE R-VALUE / σ(F): 1.38109954959 / Phase error: 17.5781487623
RfactorNum. reflection% reflection
Rfree0.183006504389 2000 4.77703203 %
Rwork0.164188376907 --
obs0.165084712623 41867 97.987221195 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.6392863715 Å2
Refinement stepCycle: LAST / Resolution: 1.55390799533→22.73975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 27 345 1986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006763175093851693
X-RAY DIFFRACTIONf_angle_d1.087678816132296
X-RAY DIFFRACTIONf_chiral_restr0.0419234563908263
X-RAY DIFFRACTIONf_plane_restr0.0044304267922292
X-RAY DIFFRACTIONf_dihedral_angle_d12.5454453274619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5539-1.59280.2043395869931160.1730484602252379X-RAY DIFFRACTION82.862836267
1.5928-1.63580.2030765829571400.1682338326862858X-RAY DIFFRACTION99.3044054323
1.6358-1.68390.204819508011430.1754731943112870X-RAY DIFFRACTION99.5703899537
1.6839-1.73830.2014310988371470.1737302477432833X-RAY DIFFRACTION99.5323981296
1.7383-1.80040.1812202662581540.1673293705132863X-RAY DIFFRACTION99.7025776603
1.8004-1.87240.1846830582121390.1685858192682865X-RAY DIFFRACTION99.8006644518
1.8724-1.95760.2016640229221460.1680286785242920X-RAY DIFFRACTION99.9348109518
1.9576-2.06070.1739019410041400.1665708162732884X-RAY DIFFRACTION99.9669421488
2.0607-2.18980.2008126836931500.1672949410982897X-RAY DIFFRACTION100
2.1898-2.35870.1998592602091440.1704835026962889X-RAY DIFFRACTION99.9011857708
2.3587-2.59570.212631343021460.175238065142905X-RAY DIFFRACTION99.9672346003
2.5957-2.97060.2063158357221450.1821155817462934X-RAY DIFFRACTION99.7085492228
2.9706-3.740.1624822134261470.157319407552935X-RAY DIFFRACTION99.5156603164
3.74-22.74220.1563027105181430.146454539292835X-RAY DIFFRACTION92.2838549737

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