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- PDB-3o0i: Structure of the human Hsp90-alpha N-domain bound to the hsp90 in... -

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Basic information

Entry
Database: PDB / ID: 3o0i
TitleStructure of the human Hsp90-alpha N-domain bound to the hsp90 inhibitor PU-H54
ComponentsHSP90AA1 protein
Keywordschaperone/Inhibitor / HSP90 Heat-Shock Proteins / chaperone-Inhibitor complex
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / dATP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / dATP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / mitochondrial transport / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / 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 / Uptake and function of diphtheria toxin / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / protein folding chaperone complex / response to unfolded protein / regulation of protein-containing complex assembly / Attenuation phase / enzyme-substrate adaptor activity / HSF1 activation / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / telomere maintenance via telomerase / axonal growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of lamellipodium assembly / nitric oxide metabolic process / protein-RNA complex assembly / skeletal muscle contraction / positive regulation of defense response to virus by host / eNOS activation / Signaling by ERBB2 / response to salt stress / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / DNA polymerase binding / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / lysosomal lumen / activation of innate immune response / Anchoring of the basal body to the plasma membrane / ESR-mediated signaling / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Constitutive Signaling by Overexpressed ERBB2 / response to cold / AURKA Activation by TPX2 / protein tyrosine kinase binding / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / cellular response to virus / Signaling by ERBB2 KD Mutants / positive regulation of protein import into nucleus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of actin dynamics for phagocytic cup formation / response to estrogen / VEGFA-VEGFR2 Pathway / Regulation of necroptotic cell death / tau protein binding / Downregulation of ERBB2 signaling / neuron migration / histone deacetylase binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / Aggrephagy
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-P54 / Heat shock protein HSP 90-alpha / HSP90AA1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsSeidler, P.M. / Gewirth, D.T.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Paralog-selective Hsp90 inhibitors define tumor-specific regulation of HER2.
Authors: Patel, P.D. / Yan, P. / Seidler, P.M. / Patel, H.J. / Sun, W. / Yang, C. / Que, N.S. / Taldone, T. / Finotti, P. / Stephani, R.A. / Gewirth, D.T. / Chiosis, G.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HSP90AA1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1112
Polymers28,7731
Non-polymers3371
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.711, 90.881, 98.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein HSP90AA1 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: HSP90AA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q2VPJ6, UniProt: P07900*PLUS
#2: Chemical ChemComp-P54 / 8-[(2,4-dimethylphenyl)sulfanyl]-3-pent-4-yn-1-yl-3H-purin-6-amine


Mass: 337.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5-fold molar excess PU-H54 ligand, 12-16% PEG-2KMME, 225-300 mM MgCl2, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 6.6 % / Number: 343719 / Rmerge(I) obs: 0.039 / Χ2: 2.11 / D res high: 1.42 Å / D res low: 50 Å / Num. obs: 52368 / % possible obs: 92.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.065098.110.0211.0557.2
2.433.0610010.0422.2937.5
2.122.4310010.0633.0827.5
1.932.1210010.0843.1537.5
1.791.9310010.1132.5297.4
1.681.7910010.1611.9137.4
1.61.6810010.2271.557.1
1.531.692.510.3051.3255.1
1.471.537710.4481.1193.9
1.421.475310.5591.462.5
ReflectionResolution: 1.47→30 Å / Num. obs: 49404 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 58.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→27.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.063 / SU ML: 0.042 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23394 2492 5 %RANDOM
Rwork0.20721 ---
obs0.20854 46912 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.47→27.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 24 267 1902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221664
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9782249
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37224.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.27415294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.62157
X-RAY DIFFRACTIONr_chiral_restr0.0730.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021225
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4681.51028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90421655
X-RAY DIFFRACTIONr_scbond_it1.3043636
X-RAY DIFFRACTIONr_scangle_it2.2164.5594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 159 -
Rwork0.321 2612 -
obs--74.23 %

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