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- PDB-4ykt: Heat Shock Protein 90 Bound to CS307 -

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Basic information

Entry
Database: PDB / ID: 4ykt
TitleHeat Shock Protein 90 Bound to CS307
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE/Inhibitor / Chaperone / PROTEIN-INHIBITOR COMPLEX / HSP 90 / CHAPERONE-Inhibitor complex
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / mitochondrial transport / protein insertion into mitochondrial outer membrane / Uptake and function of diphtheria toxin / 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 / non-chaperonin molecular chaperone ATPase / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / Sema3A PAK dependent Axon repulsion / skeletal muscle contraction / protein unfolding / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / telomere maintenance via telomerase / regulation of protein-containing complex assembly / chaperone-mediated protein complex assembly / Attenuation phase / neurofibrillary tangle assembly / RHOBTB2 GTPase cycle / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of defense response to virus by host / Recruitment of mitotic centrosome proteins and complexes / Signaling by ERBB2 / response to salt stress / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / Recruitment of NuMA to mitotic centrosomes / endocytic vesicle lumen / Anchoring of the basal body to the plasma membrane / nitric-oxide synthase regulator activity / positive regulation of cardiac muscle contraction / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / AURKA Activation by TPX2 / positive regulation of interferon-beta production / lysosomal lumen / response to cold / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / response to cocaine / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / cellular response to virus / VEGFA-VEGFR2 Pathway / Downregulation of ERBB2 signaling / histone deacetylase binding / positive regulation of protein import into nucleus / response to estrogen / Chaperone Mediated Autophagy / Aggrephagy / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / MHC class II protein complex binding / positive regulation of nitric oxide biosynthetic process / Regulation of PLK1 Activity at G2/M Transition
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-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 ...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 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4EQ / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKang, Y.N. / Stuckey, J.A.
CitationJournal: To Be Published
Title: Structure of Heat Shock Protein 90 Bound to CS307
Authors: Kang, Y.N. / Stuckey, J.A.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Derived calculations
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,1922
Polymers26,7431
Non-polymers4491
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.932, 89.063, 99.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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: 26742.840 Da / Num. of mol.: 1 / Fragment: UNP residues 2-236
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) / Strain (production host): Rosetta 2 / References: UniProt: P07900
#2: Chemical ChemComp-4EQ / 1-(5-chloro-2,4-dihydroxyphenyl)-5-({[dihydroxy(pyridin-3-yl)-lambda~4~-sulfanyl]amino}methyl)-1,3-dihydro-2H-benzimidazol-2-one


Mass: 448.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17ClN4O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 26% Peg 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.0, Cryo Conditions: 35% Peg 4000, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97852 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 24826 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.62 Å2 / Rmerge(I) obs: 0.045 / Χ2: 1.711 / Net I/av σ(I): 54.758 / Net I/σ(I): 17.4 / Num. measured all: 181076
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.887.40.40911831.09599.9
1.88-1.927.40.34512561.179100
1.92-1.957.40.28912261.20299.9
1.95-1.997.40.24812241.227100
1.99-2.047.40.212271.26999.8
2.04-2.087.40.16712331.328100
2.08-2.147.40.14312161.481100
2.14-2.197.40.12112401.672100
2.19-2.267.40.10412331.74399.9
2.26-2.337.40.09712461.83799.8
2.33-2.417.40.08312261.73899.9
2.41-2.517.40.07112361.75899.8
2.51-2.637.40.06412551.798100
2.63-2.767.30.05912311.9799.9
2.76-2.947.30.05612452.27699.9
2.94-3.167.10.05412562.66899.9
3.16-3.487.20.04412552.551100
3.48-3.997.20.03512662.209100
3.99-5.027.10.02812861.75999.8
5.02-506.60.02412861.46495

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house APO structure

Resolution: 1.85→34.45 Å / Cor.coef. Fo:Fc: 0.9538 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1263 5.09 %RANDOM
Rwork0.1795 ---
obs0.1812 24823 99.32 %-
Displacement parametersBiso max: 106.05 Å2 / Biso mean: 37.45 Å2 / Biso min: 20.81 Å2
Baniso -1Baniso -2Baniso -3
1-6.1052 Å20 Å20 Å2
2---8.4266 Å20 Å2
3---2.3214 Å2
Refine analyzeLuzzati coordinate error obs: 0.221 Å
Refinement stepCycle: final / Resolution: 1.85→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 30 190 1847
Biso mean--34.34 43.69 -
Num. residues----208
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d820SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes288HARMONIC5
X-RAY DIFFRACTIONt_it1733HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion234SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2165SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1733HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2355HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion2.79
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2332 152 5.23 %
Rwork0.1981 2757 -
all0.2 2909 -
obs--99.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1912-0.73590.28741.3284-0.13250.30510.0306-0.1486-0.0962-0.0474-0.0046-0.08840.0926-0.1509-0.0261-0.045-0.01770.0029-0.03480.021-0.0399-0.9529-33.9277-22.1241
21.06840.67240.47960.140.01230.23760.0002-0.02670.0220.0018-0.0138-0.0083-0.00480.0130.01360.01150.00620.049-0.0605-0.01010.039810.6056-25.5273-19.8347
32.93-0.26790.47440.7695-0.41810.35160.0567-0.0884-0.0762-0.137-0.0122-0.0020.0634-0.1001-0.0446-0.01160.00810.0214-0.05110.0036-0.0343-3.9338-30.2852-24.3651
40.34880.07080.87950.04460.06981.12090.0111-0.14650.02940.0056-0.0199-0.0307-0.01340.00160.0089-0.0528-0.00630.01210.077-0.0209-0.03188.4162-27.36-10.392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|16 - 73}A16 - 73
2X-RAY DIFFRACTION2{A|74 - 94}A74 - 94
3X-RAY DIFFRACTION3{A|95 - 185}A95 - 185
4X-RAY DIFFRACTION4{A|186 - 223}A186 - 223

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