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- PDB-1uy8: Human Hsp90-alpha with 9-Butyl-8-(3-trimethoxy-benzyl)-9H-purin-6... -

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Basic information

Entry
Database: PDB / ID: 1uy8
TitleHuman Hsp90-alpha with 9-Butyl-8-(3-trimethoxy-benzyl)-9H-purin-6ylamine
ComponentsHEAT SHOCK PROTEIN HSP 90-ALPHA
KeywordsCHAPERONE / HSP90 / ATPASE / PU5 / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / mitochondrial transport / protein insertion into mitochondrial outer membrane / Uptake and function of diphtheria toxin / 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 / TPR domain binding / non-chaperonin molecular chaperone ATPase / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / Sema3A PAK dependent Axon repulsion / skeletal muscle contraction / protein unfolding / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / telomere maintenance via telomerase / regulation of protein-containing complex assembly / chaperone-mediated protein complex assembly / Attenuation phase / neurofibrillary tangle assembly / RHOBTB2 GTPase cycle / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of defense response to virus by host / Recruitment of mitotic centrosome proteins and complexes / Signaling by ERBB2 / response to salt stress / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / Recruitment of NuMA to mitotic centrosomes / endocytic vesicle lumen / Anchoring of the basal body to the plasma membrane / nitric-oxide synthase regulator activity / positive regulation of cardiac muscle contraction / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / AURKA Activation by TPX2 / positive regulation of interferon-beta production / lysosomal lumen / response to cold / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / response to cocaine / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / cellular response to virus / VEGFA-VEGFR2 Pathway / Downregulation of ERBB2 signaling / histone deacetylase binding / positive regulation of protein import into nucleus / response to estrogen / Chaperone Mediated Autophagy / Aggrephagy / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / MHC class II protein complex binding / positive regulation of nitric oxide biosynthetic process / Regulation of PLK1 Activity at G2/M Transition
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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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
9-BUTYL-8-(3-METHOXYBENZYL)-9H-PURIN-6-AMINE / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsWright, L. / Barril, X. / Dymock, B. / Sheridan, L. / Surgenor, A. / Beswick, M. / Drysdale, M. / Collier, A. / Massey, A. / Davies, N. ...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.
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. / ...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.
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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)26,9132
Polymers26,6021
Non-polymers3111
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.450, 90.096, 97.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

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Components

#1: Protein HEAT SHOCK PROTEIN HSP 90-ALPHA / 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-PU5 / 9-BUTYL-8-(3-METHOXYBENZYL)-9H-PURIN-6-AMINE


Mass: 311.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOLECULAR CHAPERONE HAS ATPASE ACTIVITY

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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 20980 / % possible obs: 97.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 33.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 12.6 / % possible all: 78.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YER

1yer


Resolution: 1.98→65.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.997 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE GLU A223 WAS THE LAST RESIDUE THAT WAS VISIBLE IN ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1054 5.2 %RANDOM
Rwork0.172 ---
obs0.174 19411 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2--0.93 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.98→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 23 253 1903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221679
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9732265
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6785206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1320.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021239
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2809
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1381.51024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.15721655
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5173655
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0444.5610
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 64
Rwork0.192 1159

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