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- PDB-6gq6: Structure of human Heat shock protein 90-alpha N-terminal domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gq6 | ||||||
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Title | Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) in complex with ADP | ||||||
![]() | Heat shock protein HSP 90-alpha | ||||||
![]() | CHAPERONE / Hsp90 / NTD / alpha / complex / ADP / nucleotide | ||||||
Function / homology | ![]() 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 / 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 / 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 / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / protein unfolding / chaperone-mediated protein complex assembly / 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 / 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 / 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 / disordered domain specific binding / Regulation of PLK1 Activity at G2/M Transition / positive regulation of nitric oxide biosynthetic process / unfolded protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tassone, G. / Pozzi, C. / Mangani, S. / Botta, M. | ||||||
![]() | ![]() Title: Probing the role of Arg97 in Heat shock protein 90 N-terminal domain from the parasite Leishmania braziliensis through site-directed mutagenesis on the human counterpart. Authors: Tassone, G. / Mangani, S. / Botta, M. / Pozzi, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.1 KB | Display | ![]() |
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PDB format | ![]() | 73.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6gp4C ![]() 6gp8C ![]() 6gpfC ![]() 6gphC ![]() 6gpoC ![]() 6gppC ![]() 6gprC ![]() 6gptC ![]() 6gpwC ![]() 6gpyC ![]() 6gqrC ![]() 6gqsC ![]() 6gquC ![]() 6gr1C ![]() 6gr3C ![]() 6gr4C ![]() 6gr5C ![]() 2xk2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28773.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Precipitant: 25 % wt/vol PEG 2000, 200mM MgCl2, 100 mM sodium cacodylate, pH 6.5 Sample: Hsp90a-NTD 20 mg/mL, 10 mM ADP, 500 mM NaCl, 20 mM TRIS, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→45.47 Å / Num. obs: 10124 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 26.6 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.07 / Rrim(I) all: 0.122 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1496 / CC1/2: 0.74 / Rpim(I) all: 0.302 / Rrim(I) all: 0.523 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XK2 Resolution: 2.25→31.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.181 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.235
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.421 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.25→31.87 Å
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Refine LS restraints |
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