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- PDB-1uyg: Human Hsp90-alpha with 8-(2,5-dimethoxy-benzyl)-2-fluoro-9H-purin... -

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Basic information

Entry
Database: PDB / ID: 1uyg
TitleHuman Hsp90-alpha with 8-(2,5-dimethoxy-benzyl)-2-fluoro-9H-purin-6-ylamine
ComponentsHEAT SHOCK PROTEIN HSP 90-ALPHAHeat shock response
KeywordsCHAPERONE / HSP90 / ATPASE / PU2 / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


Signaling by ERBB2 / vRNP Assembly / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Loss of Nlp from mitotic centrosomes / HSF1-dependent transactivation / Attenuation phase / Sema3A PAK dependent Axon repulsion / HSF1 activation / HSP90 chaperone cycle for steroid hormone receptors (SHR) ...Signaling by ERBB2 / vRNP Assembly / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Loss of Nlp from mitotic centrosomes / HSF1-dependent transactivation / Attenuation phase / Sema3A PAK dependent Axon repulsion / HSF1 activation / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Scavenging by Class F Receptors / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Regulation of PLK1 Activity at G2/M Transition / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / Chaperone Mediated Autophagy / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling / ESR-mediated signaling / Downregulation of ERBB2 signaling / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Neutrophil degranulation / VEGFR2 mediated vascular permeability / Constitutive Signaling by EGFRvIII / Interleukin-4 and Interleukin-13 signaling / PIWI-interacting RNA (piRNA) biogenesis / Uptake and function of diphtheria toxin / Regulation of actin dynamics for phagocytic cup formation / Anchoring of the basal body to the plasma membrane / positive regulation of protein polymerization / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / mitochondrial transport / chaperone-mediated autophagy / positive regulation of cellular protein catabolic process / central nervous system neuron axonogenesis / TPR domain binding / dendritic growth cone / chaperone-mediated protein complex assembly / telomere maintenance via telomerase / protein unfolding / axon extension / regulation of protein ubiquitination / regulation of protein complex assembly / DNA polymerase binding / regulation of cellular protein localization / positive regulation of tau-protein kinase activity / MHC class II protein complex binding / GTPase binding / protein tyrosine kinase binding / cofactor metabolic process / axonal growth cone / response to unfolded protein / endocytic vesicle lumen / establishment of cell polarity / ciliary basal body-plasma membrane docking / protein folding chaperone / nitric-oxide synthase regulator activity / ATPase activity, coupled / response to cold / positive regulation of telomerase activity / lysosomal lumen / regulation of nitric-oxide synthase activity / ERBB2 signaling pathway / tau protein binding / regulation of cellular response to heat / melanosome / histone deacetylase binding / vascular endothelial growth factor receptor signaling pathway / receptor-mediated endocytosis / regulation of G2/M transition of mitotic cell cycle / Fc-gamma receptor signaling pathway involved in phagocytosis / scaffold protein binding / cellular response to heat / positive regulation of nitric oxide biosynthetic process / unfolded protein binding / myelin sheath / disordered domain specific binding / G2/M transition of mitotic cell cycle / response to heat / positive regulation of peptidyl-serine phosphorylation / protein folding / protein stabilization / secretory granule lumen / protein refolding / ficolin-1-rich granule lumen / ATPase activity / positive regulation of protein phosphorylation / positive regulation of protein kinase B signaling / response to antibiotic / cytokine-mediated signaling pathway / neuronal cell body / ubiquitin protein ligase binding / nucleotide binding / neutrophil degranulation / perinuclear region of cytoplasm / signal transduction
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Heat shock protein Hsp90, conserved site / Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90 family / Heat shock hsp90 proteins family signature. / Ribosomal protein S5 domain 2-type fold / Hsp90 protein / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Histidine kinase/HSP90-like ATPase superfamily
Heat shock protein HSP 90-alpha
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWright, L. / Barril, X. / Dymock, B. / Sheridan, L. / Surgenor, A. / Beswick, M. / Drysdale, M. / Collier, A. / Massey, A. / Davies, N. / Fink, A. / Fromont, C. / Aherne, W. / Boxall, K. / Sharp, S. / Workman, P. / Hubbard, R.E.
CitationJournal: Chem.Biol. / Year: 2004
Title: Structure-Activity Relationships in Purine-Based Inhibitor Binding to Hsp90 Isoforms
Authors: Wright, L. / Barril, X. / Dymock, B. / Sheridan, L. / Surgenor, A. / Beswick, M. / Drysdale, M. / Collier, A. / Massey, A. / Davies, N. / Fink, A. / Fromont, C. / Aherne, W. / Boxall, K. / Sharp, S. / Workman, P. / Hubbard, R.E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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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)26,9052
Polymers26,6021
Non-polymers3031
Water4,270237
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)66.651, 90.806, 98.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein/peptide HEAT SHOCK PROTEIN HSP 90-ALPHA / Heat shock response / HSP 86


Mass: 26601.773 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MELANOMA / Description: CLONED FROM IMAGE\:4026275 / Organ: SKIN / Plasmid: PET19 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07900
#2: Chemical ChemComp-PU2 / 8-(2,5-DIMETHOXY-BENZYL)-2-FLUORO-9H-PURIN-6-YLAMINE


Mass: 303.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14FN5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.5
Details: 25% PEG MME 2000, 0.1M NA CACODYLATE, PH6.5, 0.2M MGCL2., pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2003 / Details: OSMIC BLUE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 24040 / % possible obs: 95 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.8
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 1.7 / % possible all: 67.2

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Processing

Software
NameClassification
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YER
Resolution: 2→67.42 Å / SU B: 3.098 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.141
Details: RESIDUE GLU A223 WAS THE LAST RESIDUE THAT WAS VISIBLE IN ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21814 1036 5.1 %RANDOM
Rwork0.18334 ---
Obs-19286 94.2 %-
Displacement parametersBiso mean: 28.336 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 22 237 1895

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