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- PDB-1us7: Complex of Hsp90 and P50 -

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Basic information

Entry
Database: PDB / ID: 1us7
TitleComplex of Hsp90 and P50
Components
  • HEAT SHOCK PROTEIN HSP82Heat shock response
  • HSP90 CO-CHAPERONE CDC37
KeywordsCHAPERONE / CHAPERONE CO-CHAPERONE REGULATION / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


regulation of type II interferon-mediated signaling pathway / The NLRP3 inflammasome / HSP90-CDC37 chaperone complex / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...regulation of type II interferon-mediated signaling pathway / The NLRP3 inflammasome / HSP90-CDC37 chaperone complex / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of mitophagy in response to mitochondrial depolarization / HSF1 activation / response to oxygen levels / : / protein kinase regulator activity / protein targeting to mitochondrion / box C/D snoRNP assembly / protein folding chaperone complex / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / post-transcriptional regulation of gene expression / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of type I interferon-mediated signaling pathway / protein maturation / protein targeting / proteasome assembly / RHOBTB2 GTPase cycle / Signaling by ERBB2 / positive regulation of telomere maintenance via telomerase / heat shock protein binding / Neutrophil degranulation / Constitutive Signaling by Overexpressed ERBB2 / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Hsp90 protein binding / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Downregulation of ERBB2 signaling / kinase binding / unfolded protein binding / protein folding / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / cellular response to heat / protein-folding chaperone binding / protein refolding / scaffold protein binding / protein stabilization / protein kinase binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #250 / Cdc37, Hsp90 binding domain / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding ...Helix Hairpins - #250 / Cdc37, Hsp90 binding domain / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 / Cdc37, N-terminal domain / Cdc37 N terminal kinase binding / Helix Hairpins / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Helix non-globular / Histidine kinase/HSP90-like ATPase superfamily / Special / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSP82 / Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoe, S.M. / Ali, M.M.U. / Pearl, L.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: The Mechanism of Hsp90 Regulation by the Protein Kinase-Specific Cochaperone p50(Cdc37)
Authors: Roe, S.M. / Ali, M.M.U. / Meyer, P. / Vaughan, C.K. / Panaretou, B. / Piper, P.W. / Prodromou, C. / Pearl, L.H.
History
DepositionNov 20, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSP82
B: HSP90 CO-CHAPERONE CDC37


Theoretical massNumber of molelcules
Total (without water)55,0782
Polymers55,0782
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.759, 83.759, 148.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2059-

HOH

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Components

#1: Protein HEAT SHOCK PROTEIN HSP82 / Heat shock response / HSP82 / HSP90 / YPL240C


Mass: 24208.582 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829
#2: Protein HSP90 CO-CHAPERONE CDC37 / P50 / HSP90 CHAPERONE PROTEIN KINASE-TARGETING SUBUNIT / P50CDC37 / CDC37


Mass: 30869.100 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 125-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q16543
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: HSP82 IS AN ESSENTIAL PROTEIN THAT IS REQUIRED BY CELLS IN HIGHER CONCENTRATIONS FOR ...FUNCTION: HSP82 IS AN ESSENTIAL PROTEIN THAT IS REQUIRED BY CELLS IN HIGHER CONCENTRATIONS FOR GROWTH AT HIGHER TEMPERATURES. CDC37 CO-CHAPERONE BINDS TO NUMEROUS KINASES AND PROMOTES THEIR INTERACTION WITH THE HSP90 COMPLEX, RESULTING IN STABILIZATION AND PROMOTION OF THEIR ACTIVITY

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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: 54.6 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: CRYSTALS OF THE COMPLEX WERE GROWN FROM A MIXTURE OF N-HSP90 AND C-P50 AT A FINAL CONCENTRATION OF 0.5MM AND 0.4MM RESPECTIVELY, IN A SOLUTION CONTAINING 12% POLYETHYLENE GLYCOL 4000, 16% ...Details: CRYSTALS OF THE COMPLEX WERE GROWN FROM A MIXTURE OF N-HSP90 AND C-P50 AT A FINAL CONCENTRATION OF 0.5MM AND 0.4MM RESPECTIVELY, IN A SOLUTION CONTAINING 12% POLYETHYLENE GLYCOL 4000, 16% ISOPROPANOL AND 100MM SODIUM CITRATE, PH 6.0. CRYSTAL DROPS WERE SET UP USING THE HANGING-DROP VAPOUR DIFFUSION METHOD, INITIALLY AT 4 DEGREES C FOR 48 HOURS AND THEN TRANSFERRED TO 14 DEGREES C.
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 mMN-Hsp901drop
20.4 mMC-p501drop
312 %PEG40001reservoir
416 %isopropanol1reservoir
5100 mMsodium citrate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9202
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.3→36.3 Å / Num. obs: 26462 / % possible obs: 97.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMW

1amw


Resolution: 2.3→72.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.996 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1333 5 %RANDOM
Rwork0.185 ---
obs0.188 25125 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å20 Å2
2---0.49 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 0 176 3414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.9664423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5745396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1570.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.21479
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2175
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3791.51986
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52323205
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.25931306
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.884.51218
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 91
Rwork0.216 1839
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)
10.7418-0.01620.25650.68470.1640.7169-0.0234-0.1178-0.0287-0.03190.01530.0217-0.04230.10850.00810.10190.03220.01140.1941-0.00590.113753.728258.48124.9341
20.42190.22550.15760.4698-0.43460.4419-0.059-0.05690.0316-0.27760.0513-0.00160.16020.11510.00760.19440.0477-0.00690.1355-0.02920.14152.430853.0334-25.4091
32.6199-0.86120.21993.4618-1.1045.21610.0392-0.09950.40230.01270.05820.4613-0.4912-0.4311-0.09740.1963-0.0716-0.01490.0266-0.0070.34011.333742.5906-45.4927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 207
2X-RAY DIFFRACTION2B148 - 286
3X-RAY DIFFRACTION3B287 - 347
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 72.5 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.075

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