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Yorodumi- PDB-2h55: Structure of human Hsp90-alpha bound to the potent water soluble ... -
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-Basic information
Entry | Database: PDB / ID: 2h55 | ||||||
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Title | Structure of human Hsp90-alpha bound to the potent water soluble inhibitor PU-DZ8 | ||||||
Components | Heat shock protein HSP 90-alpha 4 | ||||||
Keywords | CHAPERONE / HSP90 / GRP94 / purine / PU3 / H64 / H71 / DZ8 | ||||||
Function / homology | Function and homology information positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane ...positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / 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 / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / protein unfolding / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / positive regulation of cell size / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of defense response to virus by host / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / activation of innate immune response / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Signaling by ERBB2 / response to salt stress / cardiac muscle cell apoptotic process / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / positive regulation of cardiac muscle contraction / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / protein tyrosine kinase binding / lysosomal lumen / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / tau protein binding / Regulation of necroptotic cell death / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Aggrephagy / Chaperone Mediated Autophagy / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / melanosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Immormino, R.M. / Gewirth, D.T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Structural and quantum chemical studies of 8-aryl-sulfanyl adenine class Hsp90 inhibitors. Authors: Immormino, R.M. / Kang, Y. / Chiosis, G. / Gewirth, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h55.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h55.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 2h55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h55_validation.pdf.gz | 785.6 KB | Display | wwPDB validaton report |
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Full document | 2h55_full_validation.pdf.gz | 787.8 KB | Display | |
Data in XML | 2h55_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 2h55_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/2h55 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/2h55 | HTTPS FTP |
-Related structure data
Related structure data | 2fwyC 2fwzSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetrict unit comprises the assumed biological molecule |
-Components
#1: Protein | Mass: 28773.145 Da / Num. of mol.: 1 / Fragment: N-terminal Domain Residues 1-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPCA / Plasmid: PET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5CAQ6, UniProt: P07900*PLUS |
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#2: Chemical | ChemComp-DZ8 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.69 % Description: THE STRUCTURE FACTOR FILE contains FRIEDEL PAIRS. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10-12% PEG-2KMME, .1-.3M MgCl2, .1 M NaCacodylate 5 molar excess of PU-DZ8, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 28, 2006 / Details: Osmic Mirrors |
Radiation | Monochromator: Copper K-alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 39220 / Num. obs: 35715 / % possible obs: 90.3 % / Observed criterion σ(F): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.059 / Net I/σ(I): 23.67 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.28 / Num. unique all: 3583 / Rsym value: 0.261 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2FWZ Resolution: 2→29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 446600.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE FRIEDEL PAIRS WERE USED FOR phasing.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.2717 Å2 / ksol: 0.31893 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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