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- PDB-7d22: Hsp90 alpha N-terminal domain in complex with a 6B compund -

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Basic information

Entry
Database: PDB / ID: 7d22
TitleHsp90 alpha N-terminal domain in complex with a 6B compund
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE/INHIBITOR / CHAPERONE-inhibitor complex
Function / homology
Function and homology information


Drug-mediated inhibition of ERBB2 signaling / ESR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / HSF1-dependent transactivation / Signaling by ERBB2 / HSF1 activation / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation ...Drug-mediated inhibition of ERBB2 signaling / ESR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / HSF1-dependent transactivation / Signaling by ERBB2 / HSF1 activation / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Downregulation of ERBB2 signaling / Attenuation phase / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Regulation of necroptotic cell death / positive regulation of cytotoxic T cell differentiation / VEGFR2 mediated vascular permeability / The role of GTSE1 in G2/M progression after G2 checkpoint / Extra-nuclear estrogen signaling / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of actin dynamics for phagocytic cup formation / Estrogen-dependent gene expression / Regulation of PLK1 Activity at G2/M Transition / VEGFA-VEGFR2 Pathway / sulfonylurea receptor binding / sperm mitochondrial sheath / dATP binding / CTP binding / positive regulation of protein polymerization / UTP binding / sperm plasma membrane / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / TPR domain binding / dendritic growth cone / non-chaperonin molecular chaperone ATPase / regulation of protein ubiquitination / positive regulation of cell size / response to unfolded protein / skeletal muscle contraction / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / neurofibrillary tangle assembly / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / nitric oxide biosynthetic process / cardiac muscle cell apoptotic process / Neutrophil degranulation / positive regulation of cardiac muscle contraction / protein folding chaperone / activation of innate immune response / positive regulation of interferon-beta production / nitric-oxide synthase regulator activity / protein tyrosine kinase binding / response to cold / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / cellular response to virus / tau protein binding / positive regulation of protein import into nucleus / response to estrogen / histone deacetylase binding / neuron migration / positive regulation of protein catabolic process / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / unfolded protein binding / melanosome / protein folding / myelin sheath / regulation of protein localization / cellular response to heat / response to heat / GTPase binding / protein refolding / scaffold protein binding / protein phosphatase binding / regulation of apoptotic process / basolateral plasma membrane / transmembrane transporter binding / protein stabilization / apical plasma membrane / response to xenobiotic stimulus / response to antibiotic / neuronal cell body / mRNA binding / ubiquitin protein ligase binding / GTP binding / perinuclear region of cytoplasm / cell surface
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 ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-GQ0 / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShin, S.C. / Kim, E.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A6A3A01095791 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Basis for Design of New Purine-Based Inhibitors Targeting the Hydrophobic Binding Pocket of Hsp90.
Authors: Shin, S.C. / El-Damasy, A.K. / Lee, J.H. / Seo, S.H. / Kim, J.H. / Seo, Y.H. / Lee, Y. / Yu, J.H. / Bang, E.K. / Kim, E.E. / Keum, G.
History
DepositionSep 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4162
Polymers24,1091
Non-polymers3071
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10410 Å2
Unit cell
Length a, b, c (Å)68.146, 89.903, 98.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
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

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP86 / Tumor-specific transplantation 86 kDa antigen / TSTA


Mass: 24109.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hsp90aa1, Hsp86, Hsp86-1, Hspca / Production host: Escherichia coli (E. coli) / References: UniProt: P07901
#2: Chemical ChemComp-GQ0 / 9-[(3-tert-butyl-1,2-oxazol-5-yl)methyl]-6-chloranyl-purin-2-amine


Mass: 306.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15ClN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.0M ammonium Sulfate, 0.1M Tris-HCl (pH8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. obs: 39322 / % possible obs: 97.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.048 / Χ2: 0.706 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.6-1.6630.34136870.442192.5
1.66-1.723.40.31937400.495193.9
1.72-1.83.80.27638570.571196.1
1.8-1.94.30.21838440.647196.6
1.9-2.0250.15839400.737198
2.02-2.175.70.10639570.804198.7
2.17-2.396.30.07740040.808199.2
2.39-2.746.80.05840320.809199.3
2.74-3.457.40.04140700.753199.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5h22

5h22


Resolution: 1.6→30.323 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 2000 5.09 %
Rwork0.1942 37322 -
obs0.1956 39322 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.43 Å2 / Biso mean: 25.8374 Å2 / Biso min: 12.44 Å2
Refinement stepCycle: final / Resolution: 1.6→30.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 21 298 1952
Biso mean--16.62 34.57 -
Num. residues----207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.63930.35551310.3342245591
1.6393-1.68360.34121370.3113254394
1.6836-1.73310.32491380.2756256795
1.7891-1.8530.26711390.2286261596
1.853-1.92720.25051430.2064263797
1.9272-2.01490.21291430.1873267998
2.0149-2.12110.20331430.1743267699
2.1211-2.25390.1971450.1704270999
2.2539-2.42790.21941460.177272399
2.4279-2.67210.2371470.1935273599
2.6721-3.05840.25241470.19862733100
3.0584-3.85210.19491480.17452776100

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