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- PDB-4yku: Heat Shock Protein 90 Bound to CS311 -

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Basic information

Entry
Database: PDB / ID: 4yku
TitleHeat Shock Protein 90 Bound to CS311
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE/Inhibitor / Chaperone / PROTEIN-INHIBITOR COMPLEX / HSP 90 / CHAPERONE-Inhibitor complex
Function / homology
Function and homology information


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 / 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 / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / 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 / dendritic growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / telomere maintenance via telomerase / protein unfolding / HSF1-dependent transactivation / response to unfolded protein / positive regulation of cell size / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / axonal growth cone / eNOS activation / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of defense response to virus by host / 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 / response to salt stress / cardiac muscle cell apoptotic process / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of cardiac muscle contraction / activation of innate immune response / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / AURKA Activation by TPX2 / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / neuron migration / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / tau protein binding / Regulation of necroptotic cell death / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Aggrephagy / Chaperone Mediated Autophagy / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / melanosome
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
6-(2-chlorophenyl)-1,3,5-triazine-2,4-diamine / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKang, Y.N. / Stuckey, J.A.
CitationJournal: To Be Published
Title: Structure of Heat Shock Protein 90 Bound to CS311
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)26,9642
Polymers26,7431
Non-polymers2221
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.067, 88.599, 100.043
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-4ER / 6-(2-chlorophenyl)-1,3,5-triazine-2,4-diamine


Mass: 221.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8ClN5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
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: 1.7→50 Å / Num. obs: 31714 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.02 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.673 / Net I/av σ(I): 40.477 / Net I/σ(I): 13.1 / Num. measured all: 226668
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.737.30.38315591.025100
1.73-1.767.30.32615821.103100
1.76-1.797.40.27515471.137100
1.79-1.837.30.24615521.22100
1.83-1.877.30.19815731.332100
1.87-1.917.30.17415781.471100
1.91-1.967.30.15115851.496100
1.96-2.027.20.13615681.731100
2.02-2.077.20.12115611.811100
2.07-2.147.10.10615851.819100
2.14-2.2270.09515711.879100
2.22-2.317.10.08815911.849100
2.31-2.417.10.08215681.816100
2.41-2.547.10.07715881.833100
2.54-2.77.10.07815982.169100
2.7-2.917.10.07615862.362100
2.91-3.27.10.06316092.005100
3.2-3.667.10.05316011.73299.9
3.66-4.617.10.04316391.87100
4.61-506.60.04516731.87397.8

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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: 1.7→34.39 Å / Cor.coef. Fo:Fc: 0.9551 / Cor.coef. Fo:Fc free: 0.9521 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.09 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 1605 5.06 %RANDOM
Rwork0.1759 ---
obs0.1769 31714 98.5 %-
Displacement parametersBiso max: 101.63 Å2 / Biso mean: 29.59 Å2 / Biso min: 14.53 Å2
Baniso -1Baniso -2Baniso -3
1-5.2293 Å20 Å20 Å2
2---5.7095 Å20 Å2
3---0.4802 Å2
Refine analyzeLuzzati coordinate error obs: 0.192 Å
Refinement stepCycle: final / Resolution: 1.7→34.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 15 242 1884
Biso mean--23.52 38.58 -
Num. residues----208
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d837SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes280HARMONIC5
X-RAY DIFFRACTIONt_it1732HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion242SEMIHARMONIC5
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_contact2206SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1732HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2353HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion2.63
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2075 123 4.89 %
Rwork0.1929 2393 -
all0.1937 2516 -
obs--98.5 %
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)
11.17420.8671-0.50220.8646-0.25910.41620.01190.11480.00460.0126-0.00220.03540.0094-0.0006-0.0097-0.0510.0084-0.01870.05680.0198-0.0364-11.9556-17.6923-32.0553
21.3811-0.02470.20580.4235-0.19671.18510.02030.08160.0430.0467-0.0242-0.0948-0.05090.02070.0039-0.0158-0.0094-0.0168-0.04730.013-0.00758.9851-10.8537-26.8981
32.26330.2804-0.08010.7143-0.05371.15360.07560.03590.10970.1019-0.03430.0089-0.0919-0.082-0.0413-0.0178-0.0026-0.009-0.05110.0112-0.0363-3.7602-14.1189-25.5188
40.5374-0.1273-0.42430.31220.12141.27960.00680.141-0.0333-0.0203-0.022-0.01710.00540.00660.0152-0.01990.0045-0.01160.0216-0.0062-0.0238.4693-17.2936-39.5539
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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