+Open data
-Basic information
Entry | Database: PDB / ID: 5j2v | ||||||
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Title | Crystal Structure of Hsp90-alpha Apo N-domain | ||||||
Components | Heat shock protein HSP 90-alphaHeat shock response | ||||||
Keywords | CHAPERONE / Apo structure | ||||||
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 / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / 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 / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / skeletal muscle contraction / protein unfolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / DNA polymerase binding / positive regulation of lamellipodium assembly / axonal growth cone / eNOS activation / endocytic vesicle lumen / 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 / positive regulation of cardiac muscle contraction / cardiac muscle cell apoptotic process / Signaling by ERBB2 / Recruitment of mitotic centrosome proteins and complexes / response to salt stress / positive regulation of telomerase activity / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / activation of innate immune response / positive regulation of interferon-beta production / response to cold / nitric-oxide synthase regulator activity / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / AURKA Activation by TPX2 / response to cocaine / VEGFR2 mediated vascular permeability / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / cellular response to virus / VEGFA-VEGFR2 Pathway / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus / response to estrogen / histone deacetylase binding / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / positive regulation of nitric oxide biosynthetic process / regulation of protein localization / disordered domain specific binding / Regulation of PLK1 Activity at G2/M Transition / melanosome / unfolded protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.59 Å | ||||||
Authors | Amaral, M. / Matias, P. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Protein conformational flexibility modulates kinetics and thermodynamics of drug binding. Authors: Amaral, M. / Kokh, D.B. / Bomke, J. / Wegener, A. / Buchstaller, H.P. / Eggenweiler, H.M. / Matias, P. / Sirrenberg, C. / Wade, R.C. / Frech, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j2v.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j2v.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 5j2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/5j2v ftp://data.pdbj.org/pub/pdb/validation_reports/j2/5j2v | HTTPS FTP |
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-Related structure data
Related structure data | 5j20C 5j27C 5j2xC 5j64C 5j6lC 5j6mC 5j6nC 5j80C 5j82C 5j86C 5j8mC 5j8uC 5j9xC C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 23205.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Plasmid: pPpARG4 / Production host: Escherichia coli (E. coli) / References: UniProt: P07900 |
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#2: 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: 3.49 Å3/Da / Density % sol: 64.76 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium fluoride, 0.1 M Bis Tris propane, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Sep 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→46.2 Å / Num. obs: 43963 / % possible obs: 99.9 % / Redundancy: 6.56 % / Biso Wilson estimate: 23.17 Å2 / Net I/σ(I): 23.71 |
-Processing
Software |
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Refinement | Resolution: 1.59→46.2 Å / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 25.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→46.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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