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

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Basic information

Entry
Database: PDB / ID: 1usv
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 / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / ATPase activator activity / protein maturation / proteasome assembly / Neutrophil degranulation / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protein folding / cellular response to heat / protein-folding chaperone binding / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / 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 / 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: 2.7 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
C: HEAT SHOCK PROTEIN HSP82
D: AHA1
E: HEAT SHOCK PROTEIN HSP82
F: AHA1
G: HEAT SHOCK PROTEIN HSP82
H: AHA1


Theoretical massNumber of molelcules
Total (without water)198,4868
Polymers198,4868
Non-polymers00
Water1,04558
1
A: HEAT SHOCK PROTEIN HSP82
B: AHA1


Theoretical massNumber of molelcules
Total (without water)49,6222
Polymers49,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: HEAT SHOCK PROTEIN HSP82
D: AHA1


Theoretical massNumber of molelcules
Total (without water)49,6222
Polymers49,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: HEAT SHOCK PROTEIN HSP82
F: AHA1


Theoretical massNumber of molelcules
Total (without water)49,6222
Polymers49,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: HEAT SHOCK PROTEIN HSP82
H: AHA1


Theoretical massNumber of molelcules
Total (without water)49,6222
Polymers49,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.397, 207.930, 84.447
Angle α, β, γ (deg.)90.00, 97.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HEAT SHOCK PROTEIN HSP82


Mass: 30502.789 Da / Num. of mol.: 4 / Fragment: MIDDLE DOMAIN, RESIDUES 272-530
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.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHSP82 IS AN ESSENTIAL PROTEIN THAT IS REQUIRED BY CELLS IN HIGH CONCENTRATIONS FOR GROWTH AT HIGHER ...HSP82 IS AN ESSENTIAL PROTEIN THAT IS REQUIRED BY CELLS IN HIGH CONCENTRATIONS FOR GROWTH AT HIGHER TEMPERATURES. THE PROTEIN IS A MOLECULAR CHAPERONE THAT HAS ATPASE 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: 2.6 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
1560 mMtri-sodium citrate dihydrate11pH6.5
220 mMTris11pH7.5
3150 mM11NaCl
41 mMEDTA11
50.5 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: 2.7→50 Å / Num. obs: 53437 / % possible obs: 98 % / Redundancy: 3 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 4.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.2 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.2

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Processing

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

1usu


Resolution: 2.7→34.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1501940.42 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 2668 5 %RANDOM
Rwork0.229 ---
obs0.229 53401 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.5505 Å2 / ksol: 0.273644 e/Å3
Displacement parametersBiso mean: 54.6 Å2
Baniso -1Baniso -2Baniso -3
1--12.98 Å20 Å210.65 Å2
2--9.03 Å20 Å2
3---3.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.7→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12725 0 0 58 12783
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scbond_it32
X-RAY DIFFRACTIONc_scangle_it4.052.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 429 5 %
Rwork0.358 8135 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 100 Å / Num. reflection obs: 53402 / Rfactor Rfree: 0.299
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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