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- PDB-5uc4: Hsp90b N-terminal domain with inhibitors -

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Basic information

Entry
Database: PDB / ID: 5uc4
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-83S / Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDeng, J. / Peng, S. / Balch, M. / Matts, R.
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 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 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)100,06514
Polymers98,3314
Non-polymers1,73410
Water9,134507
1
A: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0624
Polymers24,5831
Non-polymers4803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9703
Polymers24,5831
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0624
Polymers24,5831
Non-polymers4803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9703
Polymers24,5831
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.251, 129.251, 106.724
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: N-terminal domain (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-83S / 5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylbenzaldehyde


Mass: 309.359 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H19NO3
#3: 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
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
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: ADSC QUANTUM 315r / Detector: CCD / 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: 2.05→50 Å / Num. obs: 63537 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rsym value: 0.084 / Net I/σ(I): 26
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 6332 / Rsym value: 0.755 / % possible all: 100

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Processing

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

1uym


Resolution: 2.05→29.809 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1986 3.13 %
Rwork0.1658 --
obs0.1671 63356 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→29.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 120 507 7347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086958
X-RAY DIFFRACTIONf_angle_d0.9199395
X-RAY DIFFRACTIONf_dihedral_angle_d18.2924173
X-RAY DIFFRACTIONf_chiral_restr0.0541054
X-RAY DIFFRACTIONf_plane_restr0.0051199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10130.29191380.2234360X-RAY DIFFRACTION100
2.1013-2.15810.27361380.20044373X-RAY DIFFRACTION100
2.1581-2.22150.22541440.18944363X-RAY DIFFRACTION100
2.2215-2.29320.24291410.18374365X-RAY DIFFRACTION100
2.2932-2.37510.23381420.18374373X-RAY DIFFRACTION100
2.3751-2.47020.20711440.17974388X-RAY DIFFRACTION100
2.4702-2.58260.231480.18244381X-RAY DIFFRACTION100
2.5826-2.71860.21461370.17444359X-RAY DIFFRACTION100
2.7186-2.88880.23851400.17544393X-RAY DIFFRACTION100
2.8888-3.11170.22411420.17734382X-RAY DIFFRACTION100
3.1117-3.42440.22331410.17274407X-RAY DIFFRACTION100
3.4244-3.9190.1741430.1534395X-RAY DIFFRACTION100
3.919-4.93390.17021430.13034390X-RAY DIFFRACTION100
4.9339-29.81260.19731450.16574441X-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)
10.58770.50680.9290.53890.97761.0268-0.32590.10910.15040.21360.5641-0.0373-0.52930.5925-0.14170.66630.1622-0.01550.2057-0.05780.278919.670398.522612.8248
21.0469-1.27090.14995.87-0.88871.68230.00710.0167-0.422-0.3050.0960.55670.1633-0.0473-0.1840.2247-0.00920.00150.2391-0.01720.300618.562972.1933-6.4535
32.3773-0.32020.06062.74340.65661.8676-0.03410.03650.3399-0.1990.2846-0.7099-0.30520.5527-0.18320.2548-0.0410.03770.4689-0.12340.43642.150781.1903-3.7906
41.6567-0.64030.65412.57960.19260.7618-0.0665-0.18530.09930.29130.166-0.2585-0.31240.1926-0.08190.31220.0165-0.00160.3625-0.06970.246631.674783.11541.589
52.21620.34280.5426.04651.42085.6310.07250.1705-0.1596-0.2497-0.17490.356-0.0193-0.17480.110.22680.00680.01310.2512-0.04650.188922.246275.4955-15.3712
61.6678-0.26920.50242.0017-0.03181.1653-0.15-0.33090.2180.43110.2243-0.0576-0.27930.1295-0.06130.3480.05690.00350.3452-0.06610.221229.250385.15643.392
70.85610.5873-0.50183.69920.682.6133-0.1998-0.1587-0.37080.4030.309-0.5720.47040.3136-0.13160.27680.0903-0.01730.37410.00610.375733.106367.08323.1654
82.063-0.27910.72383.20021.44083.41590.227-0.1018-0.2999-0.32380.5213-0.70820.24650.3232-0.49370.26730.0376-0.01230.4829-0.11290.566644.76671.4026-1.3619
90.5823-0.1124-0.29412.43340.49241.75980.35240.1624-0.0736-0.4069-0.28930.42140.25410.00730.07760.40470.094-0.03850.281-0.00710.349724.067773.994433.4728
104.42530.2849-0.45483.7078-0.25732.45130.4208-0.47320.79840.2412-0.3041-0.0948-0.44260.3164-0.06860.44940.01770.03470.2974-0.03230.308131.198796.520736.637
115.08091.46132.47644.57341.52714.86460.29030.77280.0357-0.985-0.07040.5077-0.16060.0524-0.1390.62810.1817-0.03830.3551-0.01150.419121.208191.985923.1436
121.93820.5509-0.50894.589-0.73712.05870.2329-0.2178-0.16050.2402-0.2218-0.18860.11310.22260.03930.36610.06550.030.2495-0.00190.210935.902783.448634.8433
132.3153-2.6073-1.773.55040.68744.0970.0575-0.8338-0.68730.54290.03660.81390.6559-0.02970.00030.4980.00280.03660.35440.06730.389922.261474.88446.5939
142.8491-0.19650.10283.5263-0.60741.65660.1856-0.0321-0.1548-0.1335-0.05540.49990.107-0.2548-0.06850.33550.079-0.01830.2267-0.02630.276321.09182.269336.5222
153.24730.9393-0.21695.04180.02982.78880.37060.3905-0.0459-0.7651-0.4217-0.49020.27630.60370.00370.39860.17020.04450.37570.09120.264937.531784.920828.1435
160.8913-0.39710.82782.02420.3420.97290.42580.4405-0.1578-1.0094-0.3916-0.21740.19050.12770.00010.58910.21870.04150.3527-0.03350.220430.540683.821424.9545
171.8410.34140.24632.3355-0.12931.01360.1930.09530.2049-0.3793-0.01770.6303-0.1463-0.2602-0.07060.47170.1118-0.04480.2969-0.02850.515114.0795.107829.9635
180.1519-0.3123-0.29740.88690.56210.3149-0.0527-0.20060.3802-0.15140.61610.1133-0.9052-0.7876-0.20890.51570.4530.11230.4549-0.04510.401832.358277.301156.3665
192.412-0.20780.15352.09710.2792.2939-0.0574-0.071-0.0501-0.09170.0039-0.2658-0.29540.20160.03910.2215-0.03550.01740.24720.04340.233551.903767.214840.2581
202.54940.32270.55762.1902-0.02412.25590.0681-0.4059-0.37330.0161-0.0587-0.6-0.12280.3810.01210.2496-0.0451-0.00690.39340.09480.41258.83863.427947.2294
210.5925-0.8673-0.14042.2925-0.37931.68820.22530.70760.2462-0.1107-0.1862-0.4119-0.1739-0.0850.07410.2210.0686-0.01040.33470.04360.359716.790553.467225.6479
224.78821.34381.01575.08290.54022.21370.5573-0.2688-0.82010.3826-0.44060.14380.6672-0.078-0.19480.47390.0347-0.14610.28780.0260.438521.508130.188827.7516
233.79691.0005-0.68073.7882-1.25973.77270.1241.0168-0.0734-0.562-0.1091-0.29680.48390.2052-0.14470.3750.2155-0.02260.5488-0.02550.396328.13839.388714.6849
243.0821-0.8116-0.25141.9145-0.14812.34090.1610.2268-0.0039-0.0039-0.1533-0.03070.0287-0.2637-0.00270.23640.0471-0.02570.29630.02090.209116.553644.431925.8113
251.32450.16270.34341.4363-0.37921.67170.21170.5343-0.0307-0.265-0.233-0.580.27320.50820.00980.35530.15020.03430.48350.08640.457433.710844.104419.5731
262.81250.20831.30181.69631.24181.84020.66580.39-0.3641-0.14930.1658-0.339-0.00770.794-0.04350.41270.1561-0.07580.3759-0.06530.580532.929931.675323.6786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 104 )
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 177 )
7X-RAY DIFFRACTION7chain 'A' and (resid 178 through 205 )
8X-RAY DIFFRACTION8chain 'A' and (resid 206 through 217 )
9X-RAY DIFFRACTION9chain 'B' and (resid 9 through 35 )
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 88 )
12X-RAY DIFFRACTION12chain 'B' and (resid 89 through 104 )
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 118 )
14X-RAY DIFFRACTION14chain 'B' and (resid 119 through 148 )
15X-RAY DIFFRACTION15chain 'B' and (resid 149 through 159 )
16X-RAY DIFFRACTION16chain 'B' and (resid 160 through 185 )
17X-RAY DIFFRACTION17chain 'B' and (resid 186 through 217 )
18X-RAY DIFFRACTION18chain 'C' and (resid 0 through 18 )
19X-RAY DIFFRACTION19chain 'C' and (resid 19 through 163 )
20X-RAY DIFFRACTION20chain 'C' and (resid 164 through 217 )
21X-RAY DIFFRACTION21chain 'D' and (resid 9 through 35 )
22X-RAY DIFFRACTION22chain 'D' and (resid 36 through 71 )
23X-RAY DIFFRACTION23chain 'D' and (resid 72 through 88 )
24X-RAY DIFFRACTION24chain 'D' and (resid 89 through 177 )
25X-RAY DIFFRACTION25chain 'D' and (resid 178 through 205 )
26X-RAY DIFFRACTION26chain 'D' and (resid 206 through 217 )

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