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- PDB-5uci: Hsp90b N-terminal domain with inhibitors -

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Basic information

Entry
Database: PDB / ID: 5uci
TitleHsp90b N-terminal domain with inhibitors
ComponentsHeat shock protein HSP 90-betaHeat shock response
KeywordsChaperone/Inhibitor / Hsp90 inhibitor / Chaperone-Inhibitor complex
Function / homology
Function and homology information


: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / protein kinase regulator activity / positive regulation of protein localization to cell surface ...: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / protein kinase regulator activity / positive regulation of protein localization to cell surface / ATP-dependent protein binding / negative regulation of protein metabolic process / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / Uptake and function of diphtheria toxin / TPR domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / telomere maintenance via telomerase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / DNA polymerase binding / Purinergic signaling in leishmaniasis infection / supramolecular fiber organization / axonal growth cone / positive regulation of telomerase activity / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to interleukin-4 / nitric-oxide synthase regulator activity / ESR-mediated signaling / placenta development / positive regulation of cell differentiation / peptide binding / ATP-dependent protein folding chaperone / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of actin dynamics for phagocytic cup formation / kinase binding / Chaperone Mediated Autophagy / histone deacetylase binding / 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 / melanosome / unfolded protein binding / double-stranded RNA binding / protein folding / cellular response to heat / MHC class II protein complex binding / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / protein stabilization / protein dimerization activity / regulation of cell cycle / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / virion attachment to host cell / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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-874 / Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPeng, S. / Balch, M. / Matts, R. / Deng, J.
CitationJournal: Nat Commun / Year: 2018
Title: Structure-guided design of an Hsp90 beta N-terminal isoform-selective inhibitor.
Authors: Khandelwal, A. / Kent, C.N. / Balch, M. / Peng, S. / Mishra, S.J. / Deng, J. / Day, V.W. / Liu, W. / Subramanian, C. / Cohen, M. / Holzbeierlein, J.M. / Matts, R. / Blagg, B.S.J.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-beta
B: Heat shock protein HSP 90-beta
C: Heat shock protein HSP 90-beta
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,13714
Polymers98,3314
Non-polymers1,80610
Water2,090116
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A: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9883
Polymers24,5831
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0804
Polymers24,5831
Non-polymers4983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9883
Polymers24,5831
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0804
Polymers24,5831
Non-polymers4983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.273, 129.273, 107.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Heat shock protein HSP 90-beta / Heat shock response / HSP 90 / Heat shock 84 kDa / HSP84


Mass: 24582.738 Da / Num. of mol.: 4 / Fragment: UNP residues 1-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPCB / Production host: Escherichia coli (E. coli) / References: UniProt: P08238
#2: Chemical
ChemComp-874 / (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone / (1,3-dihydro-2H-isoindol-2-yl)[2,4-dihydroxy-3-(hydroxymethyl)-5-(propan-2-yl)phenyl]methanone


Mass: 327.374 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H21NO4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97922 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 28083 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rsym value: 0.139 / Net I/σ(I): 17.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2785 / Rsym value: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UYM

1uym


Resolution: 2.7→33.227 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1985 7.1 %
Rwork0.1809 --
obs0.1849 27957 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→33.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6693 0 124 116 6933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086934
X-RAY DIFFRACTIONf_angle_d1.0439364
X-RAY DIFFRACTIONf_dihedral_angle_d15.9284146
X-RAY DIFFRACTIONf_chiral_restr0.061051
X-RAY DIFFRACTIONf_plane_restr0.0061188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.76760.35961430.27631850X-RAY DIFFRACTION100
2.7676-2.84240.341410.26041866X-RAY DIFFRACTION100
2.8424-2.9260.33091430.24511827X-RAY DIFFRACTION100
2.926-3.02030.26751370.22631845X-RAY DIFFRACTION100
3.0203-3.12820.28911340.22761873X-RAY DIFFRACTION100
3.1282-3.25340.30291450.21671855X-RAY DIFFRACTION100
3.2534-3.40130.24671400.21121854X-RAY DIFFRACTION100
3.4013-3.58040.24861380.19611843X-RAY DIFFRACTION99
3.5804-3.80440.25641450.19171855X-RAY DIFFRACTION100
3.8044-4.09770.23291380.16631828X-RAY DIFFRACTION99
4.0977-4.50920.21721440.14211854X-RAY DIFFRACTION100
4.5092-5.15950.16051410.13721870X-RAY DIFFRACTION100
5.1595-6.49250.2451470.16511873X-RAY DIFFRACTION100
6.4925-33.22990.17961490.15151879X-RAY DIFFRACTION99
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)
13.57140.1571-0.36793.9322-2.42978.16360.0748-0.0679-0.12-0.95560.711-0.10850.36750.2758-0.24821.05810.23730.23710.51950.02960.777645.36256.977458.75
23.111-0.9930.81152.8440.21765.3309-0.1119-0.2218-0.0942-0.09510.19680.05760.69720.3039-0.05870.28580.0361-0.04770.28470.0180.301246.642828.028833.3862
32.95854.5898-2.26537.4866-3.7751.8976-0.25260.41090.3195-0.41010.43380.2842-0.4633-0.3664-0.12830.3599-0.0066-0.01670.43170.04660.362135.051644.347429.7381
44.95951.19960.78745.75661.09225.5715-0.75990.3464-0.6775-1.29140.66041.02580.7861-1.0862-0.08930.593-0.197-0.12820.70.13680.683118.979924.159127.5723
55.58761.08371.47325.41931.73475.83850.1558-0.74970.13920.7005-0.13470.77880.6195-0.7957-0.10590.44380.1170.11790.59270.06810.365525.485734.828241.5991
62.46640.083-1.89163.4965-0.77312.2498-0.17780.1972-0.4746-0.26110.0084-0.11830.4797-0.31660.2580.4004-0.0231-0.05890.3930.06030.263537.012323.827128.4203
76.42882.762-0.08114.8066-3.43753.2094-0.15780.31340.6434-1.00950.2215-0.8335-0.72730.2496-0.03680.4517-0.02840.06830.36190.06750.435345.516539.818117.8516
83.89871.4876-1.7134.0959-1.00163.7949-0.1191-0.1813-0.18480.06750.10360.1490.3065-0.0992-0.05570.29330.08930.010.3059-0.00710.246835.398630.598332.9502
94.98211.5067-1.40567.0099-2.21493.8223-0.4445-1.60170.28710.75440.6225-0.03540.47710.48550.21530.50180.151-0.07330.490.09070.299642.199626.030939.7026
106.02693.6831-1.62777.83461.04121.8070.3961-0.79410.11521.5529-0.03770.56080.5172-0.0709-0.00880.42110.0878-0.03460.5870.08870.322231.664631.15942.3343
117.628-1.02751.89414.8385-0.8945.49860.2299-0.49430.53780.44430.53470.7264-0.4145-0.5528-0.3720.3840.16560.04310.5007-0.00990.620428.8448.665836.4134
124.5768-0.4149-0.79174.8794-1.42385.16290.467-0.2202-0.103-0.1050.97460.9797-0.3176-1.0641-0.31640.31780.06120.04330.66950.18430.73419.695239.64335.1591
136.4872-3.6212-0.48067.51240.00352.79720.4637-0.01050.8487-0.1922-0.2976-0.74240.06590.0921-0.11970.48580.04930.09020.30910.05070.394743.291836.039669.8604
148.29234.66612.09855.61841.81391.61910.9429-1.7883-0.1061.2458-0.9483-0.52510.49430.0970.04550.47940.08850.01360.52460.06310.3538.098118.505273.6055
153.1866-1.3743-2.76814.9981-0.05957.48271.1564-1.3433-1.09810.2706-0.52430.25960.7536-0.5987-0.27960.8256-0.1351-0.0790.61260.06620.745524.027210.206571.2598
167.0887-0.2045-3.61563.305-0.9238.11370.09441.02010.0176-1.1531-0.074-0.79920.5319-0.4415-0.22910.83220.28820.05480.38590.01840.511543.880419.220957.9758
172.20621.2116-0.46232.8424-0.44842.40230.4183-0.306-0.1079-0.3699-0.231-0.11480.0895-0.0776-0.03890.44140.0163-0.05870.30770.04570.320531.598925.036867.8946
185.2697-0.67596.24283.6322-0.30357.9113-0.0005-0.15751.28080.1406-0.1484-0.784-0.4570.35150.21170.5232-0.0237-0.00190.507-0.09280.518242.982136.119681.335
193.59880.11390.54434.36912.03843.3690.23870.1807-0.1821-0.21180.1141-0.441-0.33140.128-0.19640.42750.10080.04520.2738-0.01240.431443.441129.582771.035
205.47352.8843-0.89552.93370.00524.5169-0.00460.60710.4245-1.4345-0.23970.98730.1941-1.07070.21250.65920.1839-0.14270.475-0.11990.498526.332126.145563.5453
213.4213-2.6439-0.21543.1308-0.06473.04070.63960.76450.4233-1.9925-0.47170.0572-0.3761-0.38260.19150.87440.3503-0.05320.61280.07680.209932.996733.455460.028
222.6577-0.4131-0.10674.78930.69742.19760.14210.1705-0.3701-0.21470.0617-0.90590.14670.3388-0.19240.58610.16630.06250.3911-0.01260.502247.068618.100364.4862
233.2565-2.20191.07562.7935-0.87690.35680.54160.7724-0.3312-0.26960.20010.00791.58421.2892-0.8310.92160.4179-0.11560.725-0.25550.730534.124830.859499.4437
243.9790.6903-0.48412.9613-0.09172.1448-0.17490.1346-0.08920.02540.14870.3980.5006-0.34150.05460.4212-0.0632-0.01630.3759-0.06440.295510.714743.001774.9139
255.0558-1.1846-1.9984.87490.12723.5512-0.1908-0.59570.070.52540.11080.4060.4487-0.38370.05090.3541-0.05180.02320.4476-0.02670.31389.199144.35485.3486
265.2030.0198-0.52944.7466-0.83795.1365-0.01830.61170.315-0.66080.0067-0.03580.2267-0.27340.02020.3088-0.0239-0.03960.3421-0.03480.324218.521349.348267.1648
275.47350.0203-1.30683.9915-0.29763.9498-0.1818-0.6645-0.40180.4884-0.1093-0.32740.58570.23360.15190.34330.03530.020.3905-0.01720.239318.39541.701383.3358
283.7820.9651-1.15916.8776-0.48593.0852-0.2003-0.71740.24840.76610.40640.42560.3143-0.2760.14960.33660.02450.03420.4913-0.04880.300311.046644.146286.2833
294.0183-0.1062-0.89873.6073-0.74013.58760.1392-0.21910.4816-0.5192-0.20240.8924-0.2054-0.8235-0.05440.29210.00270.01840.5817-0.08110.7155-0.717852.976980.4512
303.9799-3.08460.7334.34471.4985.68320.16730.2507-0.880.2788-0.0520.0637-0.03530.8699-0.13160.35980.0796-0.02910.389-0.11270.355351.230558.432560.6255
318.1820.5632-2.28424.122-0.11232.96110.0622-0.4829-0.29690.9083-0.0907-0.00720.20090.0564-0.02060.3550.02790.08310.3572-0.03580.36537.46971.991764.8226
325.56-0.5773-0.46221.0494-0.69833.56610.0977-0.01391.87360.0969-0.24390.4262-0.82490.41650.13370.63720.02070.09120.44820.12670.867644.505286.417657.7728
336.88790.9931.78053.0658-0.09175.3408-0.02441.21120.2127-0.1199-0.00680.437-0.3080.0483-0.06670.320.12620.08490.40480.030.476643.044572.848653.0615
346.49720.1795-0.48283.2582-1.42345.71810.4149-0.4154-0.38660.6238-0.1910.31740.0026-0.2349-0.14880.40450.05720.03520.4131-0.02730.349744.941462.800370.7816
354.384-0.5405-0.10424.7865-0.55643.45170.24620.81120.0249-0.3099-0.3814-0.37830.01380.49560.03420.28120.08860.02230.53520.03750.252649.688568.4954.2861
363.59510.75970.15843.1532-0.38753.44610.29150.26340.3588-0.0635-0.16530.6533-0.2577-0.6639-0.1210.3910.19790.03230.48-0.01270.492332.403472.513455.8649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -1:8)
2X-RAY DIFFRACTION2(chain A and resid 9:31)
3X-RAY DIFFRACTION3(chain A and resid 32:44)
4X-RAY DIFFRACTION4(chain A and resid 45:65)
5X-RAY DIFFRACTION5(chain A and resid 66:88)
6X-RAY DIFFRACTION6(chain A and resid 89:111)
7X-RAY DIFFRACTION7(chain A and resid 112:122)
8X-RAY DIFFRACTION8(chain A and resid 123:156)
9X-RAY DIFFRACTION9(chain A and resid 157:170)
10X-RAY DIFFRACTION10(chain A and resid 171:187)
11X-RAY DIFFRACTION11(chain A and resid 188:207)
12X-RAY DIFFRACTION12(chain A and resid 208:217)
13X-RAY DIFFRACTION13(chain B and resid 10:39)
14X-RAY DIFFRACTION14(chain B and resid 40:54)
15X-RAY DIFFRACTION15(chain B and resid 55:70)
16X-RAY DIFFRACTION16(chain B and resid 71:83)
17X-RAY DIFFRACTION17(chain B and resid 84:101)
18X-RAY DIFFRACTION18(chain B and resid 102:122)
19X-RAY DIFFRACTION19(chain B and resid 123:147)
20X-RAY DIFFRACTION20(chain B and resid 148:158)
21X-RAY DIFFRACTION21(chain B and resid 159:173)
22X-RAY DIFFRACTION22(chain B and resid 174:217)
23X-RAY DIFFRACTION23(chain C and resid 0:12)
24X-RAY DIFFRACTION24(chain C and resid 13:74)
25X-RAY DIFFRACTION25(chain C and resid 75:96)
26X-RAY DIFFRACTION26(chain C and resid 97:134)
27X-RAY DIFFRACTION27(chain C and resid 135:171)
28X-RAY DIFFRACTION28(chain C and resid 172:187)
29X-RAY DIFFRACTION29(chain C and resid 188:217)
30X-RAY DIFFRACTION30(chain D and resid 10:30)
31X-RAY DIFFRACTION31(chain D and resid 31:56)
32X-RAY DIFFRACTION32(chain D and resid 57:78)
33X-RAY DIFFRACTION33(chain D and resid 79:96)
34X-RAY DIFFRACTION34(chain D and resid 97:133)
35X-RAY DIFFRACTION35(chain D and resid 134:173)
36X-RAY DIFFRACTION36(chain D and resid 174:217)

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