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Yorodumi- PDB-8agl: Structure of human Heat shock protein 90-alpha N-terminal domain ... -
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-Basic information
Entry | Database: PDB / ID: 8agl | ||||||
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Title | Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) variant K112R in complex with JMC31 | ||||||
Components | Heat shock protein HSP 90-alpha | ||||||
Keywords | CHAPERONE / Hsp90 / NTD / K112R / 1 / 2 / 3-triazole-based compound / complex | ||||||
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 / telomere maintenance via telomerase / protein unfolding / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of defense response to virus by host / 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 / cardiac muscle cell apoptotic process / response to salt stress / 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 / activation of innate immune response / positive regulation of interferon-beta production / nitric-oxide synthase regulator activity / lysosomal lumen / response to cold / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / protein tyrosine kinase binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Tassone, G. / Pozzi, C. / Mazzorana, M. / Mangani, S. / Maramai, S. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Structural Characterization of Human Heat Shock Protein 90 N-Terminal Domain and Its Variants K112R and K112A in Complex with a Potent 1,2,3-Triazole-Based Inhibitor. Authors: Tassone, G. / Mazzorana, M. / Mangani, S. / Petricci, E. / Cini, E. / Giannini, G. / Pozzi, C. / Maramai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8agl.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8agl.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 8agl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8agl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8agl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8agl_validation.xml.gz | 19 KB | Display | |
Data in CIF | 8agl_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8agl ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agl | HTTPS FTP |
-Related structure data
Related structure data | 8agiC 8agjC 6gq6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28801.156 Da / Num. of mol.: 2 / Mutation: K112R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07900 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.32 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% wt/vol PEG-4000, 200 mM magnesium chloride and 100 mM TRIS-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 13, 2022 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→210.53 Å / Num. obs: 29864 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 55.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.051 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4245 / CC1/2: 0.87 / Rrim(I) all: 0.973 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GQ6 Resolution: 2.2→68.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.122 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.39 Å2 / Biso mean: 61.504 Å2 / Biso min: 31.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→68.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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