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Yorodumi- PDB-8agj: Structure of human Heat shock protein 90-alpha N-terminal domain ... -
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-Basic information
Entry | Database: PDB / ID: 8agj | ||||||
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Title | Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) variant K112A in complex with JMC31 | ||||||
Components | Heat shock protein HSP 90-alpha | ||||||
Keywords | CHAPERONE / Hsp90 / NTD / K112A / 1 / 2 / 3-triazole-based compound / complex | ||||||
Function / homology | Function and homology information 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 / positive regulation of tau-protein kinase activity / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / 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 / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / protein unfolding / HSF1 activation / regulation of protein-containing complex assembly / 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 / 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 / positive regulation of defense response to virus by host / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / response to salt stress / 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 / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / lysosomal lumen / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / 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 / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / Regulation of PLK1 Activity at G2/M Transition / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 | 8agj.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8agj.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 8agj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8agj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8agj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8agj_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 8agj_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8agj ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agj | HTTPS FTP |
-Related structure data
Related structure data | 8agiC 8aglC 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: 28715.043 Da / Num. of mol.: 2 / Mutation: K112A 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: 2.42 Å3/Da / Density % sol: 49.25 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% wt/vol PEG-2000, 200 mM magnesium chloride and 100 mM sodium cacodylate, pH 6.5 |
-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: 2.32→209.29 Å / Num. obs: 25323 / % possible obs: 99.1 % / Redundancy: 13.2 % / Biso Wilson estimate: 42.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.047 / Rrim(I) all: 0.17 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.32→2.45 Å / Rmerge(I) obs: 1.306 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3654 / CC1/2: 0.767 / Rrim(I) all: 0.047 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GQ6 Resolution: 2.32→68.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.023 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.255 / 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: 139.43 Å2 / Biso mean: 51.7 Å2 / Biso min: 19.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3634 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.32→68.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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