[English] 日本語
Yorodumi
- PDB-1uy9: Human Hsp90-alpha with 8-Benzo[1,3]dioxol-,5-ylmethyl-9-butyl-9H-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uy9
TitleHuman Hsp90-alpha with 8-Benzo[1,3]dioxol-,5-ylmethyl-9-butyl-9H-purin-6-ylamine
ComponentsHEAT SHOCK PROTEIN HSP 90-ALPHAHeat shock response
KeywordsCHAPERONE / HSP90 / ATPASE / PU6 / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


Signaling by ERBB2 / eNOS activation / Regulation of actin dynamics for phagocytic cup formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) / vRNP Assembly / HSF1 activation / Sema3A PAK dependent Axon repulsion / Recruitment of NuMA to mitotic centrosomes / VEGFR2 mediated vascular permeability / Loss of proteins required for interphase microtubule organization from the centrosome ...Signaling by ERBB2 / eNOS activation / Regulation of actin dynamics for phagocytic cup formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) / vRNP Assembly / HSF1 activation / Sema3A PAK dependent Axon repulsion / Recruitment of NuMA to mitotic centrosomes / VEGFR2 mediated vascular permeability / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Attenuation phase / VEGFA-VEGFR2 Pathway / Uptake and function of diphtheria toxin / HSF1-dependent transactivation / Interleukin-4 and Interleukin-13 signaling / 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 / Constitutive Signaling by EGFRvIII / Regulation of PLK1 Activity at G2/M Transition / Scavenging by Class F Receptors / Anchoring of the basal body to the plasma membrane / PIWI-interacting RNA (piRNA) biogenesis / Loss of Nlp from mitotic centrosomes / 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 / axon extension / protein unfolding / regulation of protein ubiquitination / DNA polymerase binding / regulation of protein complex assembly / regulation of cellular protein localization / cofactor metabolic process / positive regulation of tau-protein kinase activity / MHC class II protein complex binding / GTPase binding / protein tyrosine kinase binding / axonal growth cone / endocytic vesicle lumen / establishment of cell polarity / ciliary basal body-plasma membrane docking / response to unfolded protein / protein folding chaperone / regulation of nitric-oxide synthase activity / response to cold / lysosomal lumen / positive regulation of telomerase activity / ATPase activity, coupled / nitric-oxide synthase regulator activity / ERBB2 signaling pathway / tau protein binding / regulation of cellular response to heat / melanosome / histone deacetylase binding / vascular endothelial growth factor receptor signaling pathway / regulation of G2/M transition of mitotic cell cycle / receptor-mediated endocytosis / Fc-gamma receptor signaling pathway involved in phagocytosis / protein refolding / scaffold protein binding / unfolded protein binding / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / response to heat / myelin sheath / positive regulation of peptidyl-serine phosphorylation / G2/M transition of mitotic cell cycle / cellular response to heat / protein folding / protein stabilization / secretory granule lumen / 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
Heat shock protein Hsp90, N-terminal / Ribosomal protein S5 domain 2-type fold / Heat shock protein Hsp90, conserved site / Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90 family / Histidine kinase/HSP90-like ATPase superfamily / Heat shock hsp90 proteins family signature. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Hsp90 protein / HSP90, C-terminal domain
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSP 90-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9272
Polymers26,6021
Non-polymers3251
Water4,936274
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
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

-
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-PU6 / 8-BENZO[1,3]DIOXOL-,5-YLMETHYL-9-BUTYL-9H-


Mass: 325.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O / Water
Compound detailsMOLECULAR CHAPERONE HAS ATPASE ACTIVITY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2002 / 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: 2→30 Å / Num. obs: 20657 / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 3.4 / % possible all: 89.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YER
Resolution: 2→67.42 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.098 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.141 / 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
Rfree0.218 1036 5.1 %RANDOM
Rwork0.183 ---
Obs0.185 19286 98.2 %-
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: 28.34 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. atoms1634 0 24 274 1932
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0120.0221691
r_bond_other_d
r_angle_refined_deg1.3871.9762284
r_angle_other_deg
r_dihedral_angle_1_deg6.245207
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_chiral_restr0.0920.2263
r_gen_planes_refined0.0050.021244
r_gen_planes_other
r_nbd_refined0.2090.2804
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined0.1410.2208
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.1890.232
r_symmetry_vdw_other
r_symmetry_hbond_refined0.20.223
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.8261.51029
r_mcbond_other
r_mcangle_it1.5721664
r_mcangle_other
r_scbond_it2.3033662
r_scbond_other
r_scangle_it4.0314.5618
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 55
Rwork0.256 1218

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more