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- PDB-6n8w: Structure of Unliganded Hsp90-Beta N-Terminal Domain -

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Basic information

Entry
Database: PDB / ID: 6n8w
TitleStructure of Unliganded Hsp90-Beta N-Terminal Domain
ComponentsHeat shock protein HSP 90-betaHeat shock response
KeywordsCHAPERONE / Heat-Shock / HSP90 / Cytosolic
Function / homology
Function and homology information


: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / 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 / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / 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 / Purinergic signaling in leishmaniasis infection / supramolecular fiber organization / DNA polymerase binding / 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 / ATP-dependent protein folding chaperone / peptide binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / tau protein binding / 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 / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / unfolded protein binding / melanosome / protein folding / double-stranded RNA binding / MHC class II protein complex binding / cellular response to heat / 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
Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0922814017 Å
AuthorsHuck, J.D. / Que, N.L.S. / Gewirth, D.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA186866 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA095130 United States
CitationJournal: Proteins / Year: 2019
Title: Structures of Hsp90 alpha and Hsp90 beta bound to a purine-scaffold inhibitor reveal an exploitable residue for drug selectivity.
Authors: Huck, J.D. / Que, N.L.S. / Sharma, S. / Taldone, T. / Chiosis, G. / Gewirth, D.T.
History
DepositionNov 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)115,52537
Polymers112,4864
Non-polymers3,03933
Water95553
1
A: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8589
Polymers28,1221
Non-polymers7378
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)29,04211
Polymers28,1221
Non-polymers92110
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)29,22713
Polymers28,1221
Non-polymers1,10512
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)28,3984
Polymers28,1221
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.25, 70.249, 101.606
Angle α, β, γ (deg.)90.0, 123.451, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 28121.523 Da / Num. of mol.: 4
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) / Strain (production host): BL21 star (DE3) / References: UniProt: P08238
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl pH 8.5, MgCl2, PEG 4000, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.09→29.2 Å / Num. obs: 18636 / % possible obs: 97.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 68.7797415518 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.1
Reflection shellResolution: 3.09→3.31 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3063 / CC1/2: 0.686 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.0922814017→28.8860717038 Å / SU ML: 0.478908070321 / Cross valid method: FREE R-VALUE / σ(F): 1.35078714894 / Phase error: 31.9436554771
RfactorNum. reflection% reflection
Rfree0.285876337001 1851 9.9366544986 %
Rwork0.225043687799 --
obs0.231030896435 18628 97.6156788765 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.509413689 Å2
Refinement stepCycle: LAST / Resolution: 3.0922814017→28.8860717038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6627 0 198 53 6878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001941380887956915
X-RAY DIFFRACTIONf_angle_d0.5102294259679333
X-RAY DIFFRACTIONf_chiral_restr0.02163862155451073
X-RAY DIFFRACTIONf_plane_restr0.002402003060831183
X-RAY DIFFRACTIONf_dihedral_angle_d10.91304722272430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0923-3.17580.4070802397261130.33545830875988X-RAY DIFFRACTION75.0511247444
3.1758-3.26910.3897007268531390.3108855384931309X-RAY DIFFRACTION99.1780821918
3.2691-3.37450.3711975912841460.3086406356191297X-RAY DIFFRACTION99.3117687543
3.3745-3.49490.335828167271450.2868429497281308X-RAY DIFFRACTION99.4524298426
3.4949-3.63460.3183699626911440.2699325973511310X-RAY DIFFRACTION99.7940974605
3.6346-3.79960.3083391424441450.2450851826491287X-RAY DIFFRACTION99.3754337266
3.7996-3.99950.28594187171460.2279482126741290X-RAY DIFFRACTION99.7915218902
3.9995-4.24930.2855378489451420.2170056316251342X-RAY DIFFRACTION99.865410498
4.2493-4.57620.2513813188961470.1860320069371323X-RAY DIFFRACTION99.8641304348
4.5762-5.03460.278896384311390.1956063286831318X-RAY DIFFRACTION99.5898838004
5.0346-5.75810.2595375706721450.2208975052811314X-RAY DIFFRACTION99.5225102319
5.7581-7.23570.274860199021490.2387330039711339X-RAY DIFFRACTION99.7319034853
7.2357-28.88730.2317832124181510.1667726015181352X-RAY DIFFRACTION98.6220472441

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