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- PDB-4ykw: Heat Shock Protein 90 Bound to CS312 -

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Basic information

Entry
Database: PDB / ID: 4ykw
TitleHeat Shock Protein 90 Bound to CS312
ComponentsHeat shock protein HSP 90-alphaHeat shock response
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 / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / 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 / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / skeletal muscle contraction / protein unfolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / DNA polymerase binding / positive regulation of lamellipodium assembly / axonal growth cone / eNOS activation / endocytic vesicle lumen / 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 / positive regulation of cardiac muscle contraction / cardiac muscle cell apoptotic process / Signaling by ERBB2 / Recruitment of mitotic centrosome proteins and complexes / response to salt stress / positive regulation of telomerase activity / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / activation of innate immune response / positive regulation of interferon-beta production / response to cold / nitric-oxide synthase regulator activity / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / AURKA Activation by TPX2 / response to cocaine / VEGFR2 mediated vascular permeability / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / cellular response to virus / VEGFA-VEGFR2 Pathway / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus / response to estrogen / histone deacetylase binding / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / positive regulation of nitric oxide biosynthetic process / regulation of protein localization / disordered domain specific binding / Regulation of PLK1 Activity at G2/M Transition / melanosome / unfolded protein 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
Chem-4ES / 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 CS312
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
B: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0154
Polymers53,4862
Non-polymers5292
Water3,873215
1
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0082
Polymers26,7431
Non-polymers2651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0082
Polymers26,7431
Non-polymers2651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.928, 51.853, 56.703
Angle α, β, γ (deg.)68.430, 86.650, 71.500
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock response / 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.: 2 / 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-4ES / 4-(2-chloro-4-nitrophenyl)-6-methylpyrimidin-2-amine


Mass: 264.668 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9ClN4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% Peg 1000, 0.1 M Tris pH 7.0, 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-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 36735 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.65 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.918 / Net I/av σ(I): 21.933 / Net I/σ(I): 7.7 / Num. measured all: 144968
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.883.60.49518160.70596.2
1.88-1.923.90.41818110.69796.6
1.92-1.9540.36918030.75397
1.95-1.9940.30418360.75897
1.99-2.0440.26118110.74897.1
2.04-2.0840.23918460.8297.4
2.08-2.1440.19217730.80497.4
2.14-2.1940.16818470.82597.6
2.19-2.263.90.14218520.9397.6
2.26-2.3340.13118170.89997.8
2.33-2.4140.11518520.94897.9
2.41-2.5140.10418240.98498.4
2.51-2.6340.09518360.98598.1
2.63-2.7640.0818580.98698.4
2.76-2.9440.07118581.01598.7
2.94-3.1640.05918471.15298.8
3.16-3.4840.04718631.07699.1
3.48-3.993.90.04218641.44799.1
3.99-5.0240.02818560.88499.4
5.02-503.90.02818650.8899.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house APO Structure

Resolution: 1.85→45.71 Å / Cor.coef. Fo:Fc: 0.9486 / Cor.coef. Fo:Fc free: 0.9274 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1834 4.99 %RANDOM
Rwork0.1956 ---
obs0.1973 36735 97.73 %-
Displacement parametersBiso max: 101.16 Å2 / Biso mean: 33.14 Å2 / Biso min: 12.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.1941 Å20.172 Å21.2757 Å2
2--0.0465 Å20.3014 Å2
3---0.1476 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: final / Resolution: 1.85→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 36 215 3562
Biso mean--27.83 37.8 -
Num. residues----426
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1651SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes551HARMONIC5
X-RAY DIFFRACTIONt_it3475HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion479SEMIHARMONIC5
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_contact4153SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3475HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4717HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion2.83
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2044 140 4.84 %
Rwork0.2139 2751 -
all0.2134 2891 -
obs--97.73 %
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)
10.93420.73570.14120.6634-0.59710.3111-0.0018-0.01760.03550.0053-0.0074-0.0004-0.0260.00870.0092-0.01570.0089-0.0597-0.0418-0.05460.032518.29821.9897-4.7523
20.3125-0.37120.09260.8211-0.02830.5978-0.0232-0.0478-0.0090.0050.0157-0.0241-0.0338-0.07330.0075-0.0657-0.005-0.00050.04770.0199-0.020312.3038-18.3696-3.0648
30.2468-0.0092-0.35340.49690.1506-0.1537-0.009-0.02330.01130.0035-0.00570.004-0.0371-0.02050.0147-0.02950.02890.00750.0243-0.01320.01489.8475-7.3544-2.9678
40.06350.05660.0435-0.03660.02820.13580.0008-0.00210.00090.0021-0.0047-0.0011-0.0020.00080.0039-0.0137-0.0245-0.02170.0399-0.006-0.024725.2587-3.30639.9965
50.0335-0.37270.02050.76930.03060.497-0.0006-0.01760.02130.0235-0.00050.008-0.0622-0.01880.001-0.0295-0.0011-0.03520.004-0.00310.01115.0893-6.0961-3.706
61.4082-0.14470.31490.58090.23950.6816-0.038-0.0252-0.0278-0.09-0.0186-0.0581-0.0346-0.00840.0566-0.0576-0.00550.0116-0.0150.03320.024420.8333-15.4676-8.5069
70.64880.6932-0.3780.89070.054-0.1427-0.01890.0128-0.0017-0.04670.0240.00820.0062-0.0046-0.00510.0187-0.0326-0.0018-0.0366-0.05330.01125.1059-26.473726.7506
8-0.1443-0.21390.09470.1746-0.03770.0679-0.00280.0129-0.018-0.0180.0095-0.0117-0.01340.0191-0.00670.0529-0.03490.05820.00130.0009-0.050822.0872-17.371522.8363
90.51690.5254-0.33470.3257-0.0083-0.0308-0.01360.00520.0278-0.0207-0.00310.040.0008-0.00520.01670.02340.0067-0.0005-0.03770.04540.002412.7706-3.659627.0759
10-0.0931-0.06320.30050.0158-0.14370.0772-0.00240.04280.0044-0.0282-0.0003-0.00220.01520.00120.00270.0154-0.0292-0.04750.0170.03630.000910.8814-19.221217.7921
111.9421.8107-0.29891.70620.21450.2463-0.05360.02780.0173-0.16440.0165-0.00650.062-0.01880.0371-0.02870.00260.0005-0.05850.0141-0.003913.3798-17.313129.5652
120.24690.11430.03160.0321-0.04860.0228-0.00210.0045-0.0008-0.00410.0057-0.0082-0.00050.0066-0.00360.00940.00440.01040.00260.019-0.009725.3017-6.73527.921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|11 - 40}A11 - 40
2X-RAY DIFFRACTION2{A|41 - 87}A41 - 87
3X-RAY DIFFRACTION3{A|88 - 111}A88 - 111
4X-RAY DIFFRACTION4{A|112 - 127}A112 - 127
5X-RAY DIFFRACTION5{A|128 - 169}A128 - 169
6X-RAY DIFFRACTION6{A|170 - 223}A170 - 223
7X-RAY DIFFRACTION7{B|11 - 36}B11 - 36
8X-RAY DIFFRACTION8{B|37 - 56}B37 - 56
9X-RAY DIFFRACTION9{B|57 - 90}B57 - 90
10X-RAY DIFFRACTION10{B|91 - 127}B91 - 127
11X-RAY DIFFRACTION11{B|128 - 207}B128 - 207
12X-RAY DIFFRACTION12{B|208 - 223}B208 - 223

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