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- PDB-7d24: Hsp90 alpha N-terminal domain in complex with a 4B compund -

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Basic information

Entry
Database: PDB / ID: 7d24
TitleHsp90 alpha N-terminal domain in complex with a 4B 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 / sperm mitochondrial sheath / sulfonylurea receptor binding / 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 / non-chaperonin molecular chaperone ATPase / dendritic growth cone / positive regulation of cell size / regulation of protein ubiquitination / response to unfolded protein / skeletal muscle contraction / regulation of postsynaptic membrane neurotransmitter receptor levels / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / 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 / cardiac muscle cell apoptotic process / nitric oxide biosynthetic process / Neutrophil degranulation / positive regulation of cardiac muscle contraction / nitric-oxide synthase regulator activity / protein folding chaperone / activation of innate immune response / positive regulation of interferon-beta production / response to cold / protein tyrosine kinase binding / ATP-dependent protein folding chaperone / response to cocaine / brush border membrane / cellular response to virus / tau protein binding / histone deacetylase binding / positive regulation of protein import into nucleus / response to estrogen / positive regulation of protein catabolic process / neuron migration / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / 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 / : / basolateral plasma membrane / regulation of apoptotic process / 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
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 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-GQ3 / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)24,4182
Polymers24,1091
Non-polymers3091
Water5,927329
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 area10610 Å2
Unit cell
Length a, b, c (Å)67.351, 89.891, 98.591
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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-GQ3 / 9-[(3-tert-butyl-1,2-oxazol-5-yl)methyl]-6-chloranyl-purin-2-amine


Mass: 308.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17ClN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 3.19 Å3/Da / Density % sol: 61.48 %
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: 1.547→50 Å / Num. obs: 42003 / % possible obs: 95.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.04 / Χ2: 0.811 / Net I/σ(I): 20.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.55-1.614.20.20635910.717182.8
1.61-1.6750.18140870.763194.2
1.67-1.755.40.14541300.803195.4
1.75-1.845.80.1141580.836195.8
1.84-1.956.30.07942480.87197.3
1.95-2.16.80.05942390.884197.5
2.1-2.327.20.04643090.853198.1
2.32-2.657.40.03943310.805198.7
2.65-3.347.70.03444040.772199.2
3.34-507.70.03145060.764197.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H22

5h22


Resolution: 1.55→34.957 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 2000 4.76 %
Rwork0.1803 40003 -
obs0.1811 42003 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.7 Å2 / Biso mean: 22.0052 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 1.55→34.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 21 329 1992
Biso mean--14.26 31.65 -
Num. residues----209
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.58550.26691110.2149223476
1.5855-1.62840.2271380.2002274893
1.6284-1.67630.21941400.1938280895
1.6763-1.73040.23041420.1877283095
1.7304-1.79230.21971400.1876280496
1.7923-1.8640.19151450.1794288796
1.864-1.94890.17611430.1712287197
1.9489-2.05160.18311450.175291297
2.0516-2.18010.18541460.1745291398
2.1801-2.34840.19841470.174293498
2.3484-2.58470.20181490.1846297299
2.5847-2.95850.21021490.1898298099
2.9585-3.72670.20231510.176302799
3.7267-34.9570.17991540.1752308397

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