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- PDB-6b9a: Hsp90-alpha N-domain bound to NPCA -

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Basic information

Entry
Database: PDB / ID: 6b9a
TitleHsp90-alpha N-domain bound to NPCA
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE/INHIBITOR / Chaperone / Hsp90 / Inhibitor / CHAPERONE-INHIBITOR 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 / Uptake and function of diphtheria toxin / Rho GDP-dissociation inhibitor binding / 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 / positive regulation of telomerase activity / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of defense response to virus by host / positive regulation of cardiac muscle contraction / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / response to salt stress / 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 / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / 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
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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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
N-PROPYL CARBOXYAMIDO ADENOSINE / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65381 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 NPCA
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
B: Heat shock protein HSP 90-alpha
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8693
Polymers57,5462
Non-polymers3221
Water8,611478
1
B: Heat shock protein HSP 90-alpha


Theoretical massNumber of molelcules
Total (without water)28,7731
Polymers28,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0952
Polymers28,7731
Non-polymers3221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.448, 89.385, 99.29
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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.: 2
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-PA7 / N-PROPYL CARBOXYAMIDO ADENOSINE


Mass: 322.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Bis-Tris Propane pH 6.4, MgCl2, PEG 2000 MME. Soak crystals with NPCA

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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, 2017
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 68453 / % possible obs: 99.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 27.0568978781 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 29.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.84 / % possible all: 99.5

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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: 1.65381→43.4152 Å / SU ML: 0.145340212517 / Cross valid method: FREE R-VALUE / σ(F): 1.38670747008 / Phase error: 19.6488821736
RfactorNum. reflection% reflection
Rfree0.190582895583 2000 2.92406210708 %
Rwork0.163953451081 --
obs0.164742267313 68398 98.8581835 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.4427885326 Å2
Refinement stepCycle: LAST / Resolution: 1.65381→43.4152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 23 478 3696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01338555845623322
X-RAY DIFFRACTIONf_angle_d1.67716256984498
X-RAY DIFFRACTIONf_chiral_restr0.0723617131956524
X-RAY DIFFRACTIONf_plane_restr0.00685046566259565
X-RAY DIFFRACTIONf_dihedral_angle_d13.06044308161202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65381-1.69520.2707039510881340.2120123199954445X-RAY DIFFRACTION94.412371134
1.6952-1.7410.2504057547971420.2037785263454711X-RAY DIFFRACTION99.2230627684
1.741-1.79220.2213166789511410.190120059974696X-RAY DIFFRACTION99.3427808585
1.7922-1.85010.1998586757841420.1826076553184706X-RAY DIFFRACTION99.2628992629
1.8501-1.91620.2066082624041420.1805914988964725X-RAY DIFFRACTION99.5093028011
1.9162-1.99290.2024466542011430.1683314537664727X-RAY DIFFRACTION99.4283380972
1.9929-2.08360.2211844552371430.1715307018724751X-RAY DIFFRACTION99.33022123
2.0836-2.19350.1905692689221410.1553380379714700X-RAY DIFFRACTION98.8968335036
2.1935-2.33090.1801384241881430.1680581186124734X-RAY DIFFRACTION99.4291539246
2.3309-2.51090.2203259371351450.1649390083124796X-RAY DIFFRACTION99.5366639807
2.5109-2.76350.2146273212671430.1722533524874771X-RAY DIFFRACTION99.2727272727
2.7635-3.16330.2100809074891440.1660029767844791X-RAY DIFFRACTION99.0566037736
3.1633-3.9850.1518185792091470.1492179890914844X-RAY DIFFRACTION99.244382581
3.985-43.41520.1779028487221500.1591565236495001X-RAY DIFFRACTION98.0769230769

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