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- PDB-4yky: Heat Shock Protein 90 Bound to CS319 -

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Basic information

Entry
Database: PDB / ID: 4yky
TitleHeat Shock Protein 90 Bound to CS319
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 / 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 / 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 / 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 / : / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of defense response to virus by host / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / 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 / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / positive regulation of protein import into nucleus / Chaperone Mediated Autophagy / 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
(2,4-dihydroxyphenyl)(4-hydroxyphenyl)methanone / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsKang, Y.N. / Stuckey, J.A.
CitationJournal: To Be Published
Title: Structure of Heat Shock Protein 90 Bound to CS319
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,0653
Polymers26,7431
Non-polymers3222
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.885, 88.878, 99.565
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-4EU / (2,4-dihydroxyphenyl)(4-hydroxyphenyl)methanone


Mass: 230.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
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: 1.78→50 Å / Num. obs: 27789 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 27.71 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.97 / Net I/av σ(I): 44.775 / Net I/σ(I): 15.1 / Num. measured all: 198037
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.78-1.817.30.40413841.29100
1.81-1.847.30.3413721.447100
1.84-1.887.30.30813431.562100
1.88-1.927.20.25813871.734100
1.92-1.967.20.22313981.833100
1.96-27.20.20213522.034100
2-2.057.10.17613922.172100
2.05-2.117.10.15613882.222100
2.11-2.1770.1313572.451100
2.17-2.2470.11813942.433100
2.24-2.3270.10713732.42100
2.32-2.427.10.09713742.306100
2.42-2.537.10.08713782.296100
2.53-2.667.20.07913972.207100
2.66-2.837.10.0714002.21100
2.83-3.047.20.06213892.131100
3.04-3.357.20.05314082.025100
3.35-3.837.20.04614181.84100
3.83-4.837.10.03814201.499100
4.83-506.70.03714651.36696.8

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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: 1.78→34.41 Å / Cor.coef. Fo:Fc: 0.9639 / Cor.coef. Fo:Fc free: 0.9607 / SU R Cruickshank DPI: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.09 / SU Rfree Cruickshank DPI: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 1396 5.02 %RANDOM
Rwork0.1662 ---
obs0.1673 27789 99.37 %-
Displacement parametersBiso max: 104.85 Å2 / Biso mean: 30.89 Å2 / Biso min: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.0381 Å20 Å20 Å2
2--0.0276 Å20 Å2
3----2.0658 Å2
Refine analyzeLuzzati coordinate error obs: 0.179 Å
Refinement stepCycle: final / Resolution: 1.78→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 23 214 1864
Biso mean--40.07 40.48 -
Num. residues----208
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d813SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes272HARMONIC5
X-RAY DIFFRACTIONt_it1711HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion233SEMIHARMONIC5
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_contact2173SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1711HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2314HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion2.68
LS refinement shellResolution: 1.78→1.85 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.1935 127 4.6 %
Rwork0.1654 2636 -
all0.1668 2763 -
obs--99.37 %
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)
10.8917-0.84581.17060.9835-0.32320.38450.0043-0.09510.0082-0.01010.00850.0494-0.0077-0.0076-0.0128-0.04010.00110.0240.0350.0351-0.0219-11.7736-26.7977-17.9385
21.3836-0.1722-0.31470.4209-0.031.5060.01970.0019-0.0207-0.0441-0.0356-0.09070.06330.02830.0159-0.00940.00830.02-0.05230.0129-0.00998.8722-33.7497-23.0214
32.0991-0.26310.01220.848-0.03621.24680.07520.0162-0.092-0.0739-0.03710.04720.0845-0.0568-0.038-0.02340.01260.0058-0.06060.0107-0.0316-3.9715-30.1538-24.4989
41.1506-0.02320.36990.35260.1381.63890.0005-0.11470.05020.0218-0.0144-0.0209-0.010.01140.0139-0.0048-0.00970.0096-0.0118-0.0058-0.02448.3428-27.2609-10.5885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|16 - 41}A16 - 41
2X-RAY DIFFRACTION2{A|42 - 95}A42 - 95
3X-RAY DIFFRACTION3{A|96 - 185}A96 - 185
4X-RAY DIFFRACTION4{A|186 - 223}A186 - 223

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