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- PDB-6b99: Hsp90-alpha N-domain bound to NECA -

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Basic information

Entry
Database: PDB / ID: 6b99
TitleHsp90-alpha N-domain bound to NECA
ComponentsHeat shock protein HSP 90-alpha
KeywordsChaperone/Inhibitor / Chaperone / Hsp90 / Inhibitor / Chaperone-Inhibitor complex
Function / homology
Function and homology information


sulfonylurea receptor binding / sperm mitochondrial sheath / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sulfonylurea receptor binding / sperm mitochondrial sheath / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / protein insertion into mitochondrial outer membrane / 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 / TPR domain binding / dendritic growth cone / Assembly and release of respiratory syncytial virus (RSV) virions / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / Sema3A PAK dependent Axon repulsion / protein unfolding / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / HSF1 activation / regulation of protein-containing complex assembly / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / neurofibrillary tangle assembly / axonal growth cone / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / positive regulation of telomere maintenance via telomerase / cardiac muscle cell apoptotic process / 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 / activation of innate immune response / lysosomal lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of interferon-beta production / nitric-oxide synthase regulator activity / protein tyrosine kinase binding / response to cold / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Regulation of necroptotic cell death / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Downregulation of ERBB2 signaling / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Chaperone Mediated Autophagy / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / tau protein binding / Aggrephagy / positive regulation of protein import into nucleus / VEGFA-VEGFR2 Pathway / response to estrogen / histone deacetylase binding / The role of GTSE1 in G2/M progression after G2 checkpoint / neuron migration / Regulation of PLK1 Activity at G2/M Transition / positive regulation of protein catabolic process / positive regulation of nitric oxide biosynthetic process
Similarity search - Function
Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-ETHYL-5'-CARBOXAMIDO ADENOSINE / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.60237722156 Å
AuthorsHuck, J.D. / Gewirth, D.T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA186866 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA095130 United States
Avon Foundation02-2016-079 United States
Goode Foundation of Buffalo United States
CitationJournal: To Be Published
Title: Hsp90-alpha N-domain bound to NECA
Authors: Huck, J.D. / Gewirth, D.T.
History
DepositionOct 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0812
Polymers28,7731
Non-polymers3081
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-0 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.547, 90.077, 98.409
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / ...Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 28773.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: Escherichia coli (E. coli) / References: UniProt: P07900
#2: Chemical ChemComp-NEC / N-ETHYL-5'-CARBOXAMIDO ADENOSINE


Mass: 308.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Bis Tris Propane pH 6.4, MgCl2, PEG 2000 MME. Soak with NECA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 37663 / % possible obs: 99.2 % / Redundancy: 6 % / Biso Wilson estimate: 16.9584459994 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 26.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.8 / CC1/2: 0.791 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YER

1yer


Resolution: 1.60237722156→35.8908695175 Å / SU ML: 0.144269740969 / Cross valid method: FREE R-VALUE / σ(F): 1.3853282991 / Phase error: 17.5572786825
RfactorNum. reflection% reflection
Rfree0.182737972728 2000 5.31067445566 %
Rwork0.164343939421 --
obs0.165339757759 37660 99.006256901 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.583791812 Å2
Refinement stepCycle: LAST / Resolution: 1.60237722156→35.8908695175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 22 280 1916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006160250603691735
X-RAY DIFFRACTIONf_angle_d1.03239568922365
X-RAY DIFFRACTIONf_chiral_restr0.0424194610987277
X-RAY DIFFRACTIONf_plane_restr0.00412218568137300
X-RAY DIFFRACTIONf_dihedral_angle_d12.671468151635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6024-1.64240.2373249879951380.1949559946122451X-RAY DIFFRACTION96.1381359079
1.6424-1.68690.1987684770511410.1855630579682521X-RAY DIFFRACTION99.7377294867
1.6869-1.73650.2215592684221420.1806889865842531X-RAY DIFFRACTION99.5530726257
1.7365-1.79250.1988175576631420.1793416311832532X-RAY DIFFRACTION99.5903165736
1.7925-1.85660.1929271933321420.1736664252472540X-RAY DIFFRACTION99.5545657016
1.8566-1.93090.2171794428791420.1686767691452530X-RAY DIFFRACTION99.7759522031
1.9309-2.01880.1872897108161440.1614325151412562X-RAY DIFFRACTION99.852398524
2.0188-2.12520.169142549591420.1545140852952539X-RAY DIFFRACTION99.7767026424
2.1252-2.25840.1609724092511440.1597387090032554X-RAY DIFFRACTION99.3006993007
2.2584-2.43270.1852892200651420.1639173334432541X-RAY DIFFRACTION99.6656760773
2.4327-2.67740.1955096784681460.167656685062589X-RAY DIFFRACTION99.5994173343
2.6774-3.06470.1812561233461420.1738076029112544X-RAY DIFFRACTION98.4243312569
3.0647-3.86050.164208936991430.1585492683572551X-RAY DIFFRACTION97.4321880651
3.8605-35.89990.1796238464551500.1552830504462675X-RAY DIFFRACTION97.8863478863

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