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- PDB-1usu: The Structure of the complex between Aha1 and HSP90 -

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Basic information

Entry
Database: PDB / ID: 1usu
TitleThe Structure of the complex between Aha1 and HSP90
Components
  • AHA1
  • HEAT SHOCK PROTEIN HSP82
KeywordsCHAPERONE / CHAPERONE-COMPLEX / ACTIVATOR / HSP90
Function / homology
Function and homology information


The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein targeting to mitochondrion / ATPase activator activity / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / protein maturation / ATP-dependent protein folding chaperone / protein import into nucleus / unfolded protein binding / protein folding / protein-folding chaperone binding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / protein-containing complex / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Activator of Hsp90 ATPase Aha1, N-terminal domain / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, Aha1 / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, N-terminal / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Activator of Hsp90 ATPase homologue 1-like ...Activator of Hsp90 ATPase Aha1, N-terminal domain / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, Aha1 / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, N-terminal / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START-like domain superfamily / Ribosomal Protein S5; domain 2 / 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 ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSP82 / Hsp90 co-chaperone AHA1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMeyer, P. / Roe, S.M. / Pearl, L.H.
CitationJournal: Embo J. / Year: 2004
Title: Structural Basis for Recruitment of the ATPase Activator Aha1 to the Hsp90 Chaperone Machinery.
Authors: Meyer, P. / Prodromou, C. / Liao, C. / Hu, B. / Roe, S.M. / Vaughan, C.K. / Vlasic, I. / Panaretou, B. / Piper, P.W. / Pearl, L.H.
History
DepositionDec 1, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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: AHA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6983
Polymers49,6052
Non-polymers921
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.940, 37.920, 111.260
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEAT SHOCK PROTEIN HSP82


Mass: 30486.727 Da / Num. of mol.: 1 / Fragment: MIDDLE DOMAIN, RESIDUES 273-530
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 AHA1


Mass: 19118.715 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q12449
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 292 K / Method: microbatch / pH: 6.5
Details: CRYSTALS GREW FROM A MIXTURE OF MIDDLE DOMAIN HSP90 AND N- TERMINAL AHA1 AT A FINAL CONCENTRATION OF 110 UM AND 165 UM, RESPECTIVELY, IN A SOLUTION CONTAINING 90 MM AMMONIUM SULPHATE, 13.5% ...Details: CRYSTALS GREW FROM A MIXTURE OF MIDDLE DOMAIN HSP90 AND N- TERMINAL AHA1 AT A FINAL CONCENTRATION OF 110 UM AND 165 UM, RESPECTIVELY, IN A SOLUTION CONTAINING 90 MM AMMONIUM SULPHATE, 13.5% (W/V) PEG8K AND 45 MM SODIUM CACODYLATE PH 6.5 IN UNDER-OIL MICROBATCH EXPERIMENTS AT 19C.
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 6.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
190 mMammonium sulfate11
213.5 %(w/v)PEG800011
345 mMsodium cacodylate11pH6.5
420 mMTris11pH7.5
5150 mM11NaCl
61 mMEDTA11
70.5 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 26832 / % possible obs: 99.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.6
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 3.2 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 2.15 Å / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge F obs: 0.089
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK7

1hk7


Resolution: 2.15→31.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1001963.23 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1339 5 %RANDOM
Rwork0.213 ---
obs0.213 26818 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5145 Å2 / ksol: 0.340679 e/Å3
Displacement parametersBiso mean: 48.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å22.23 Å2
2---0.78 Å20 Å2
3----0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.15→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 6 227 3301
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it2.892
X-RAY DIFFRACTIONc_scbond_it3.742
X-RAY DIFFRACTIONc_scangle_it4.892.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 208 4.7 %
Rwork0.241 4221 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HEP_GOL.PARHEP_GOL.TOP
Refinement
*PLUS
Lowest resolution: 100 Å / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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