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- PDB-1am1: ATP BINDING SITE IN THE HSP90 MOLECULAR CHAPERONE -

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Basic information

Entry
Database: PDB / ID: 1am1
TitleATP BINDING SITE IN THE HSP90 MOLECULAR CHAPERONE
ComponentsHEAT SHOCK PROTEIN 90
KeywordsCHAPERONE / NUCLEOTIDE BINDING SITE
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 / protein targeting to mitochondrion ...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 / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / Neutrophil degranulation / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / 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
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 2 Å
AuthorsPearl, L.H. / Roe, S.M. / Prodromou, C.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone
Authors: Prodromou, C. / Roe, S.M. / O'Brien, R. / Ladbury, J.E. / Piper, P.W. / Pearl, L.H.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: A Molecular Clamp in the Crystal Structure of the N-Terminal Domain of the Yeast Hsp90 Chaperone
Authors: Prodromou, C. / Roe, S.M. / Piper, P.W. / Pearl, L.H.
History
DepositionJun 20, 1997Processing site: BNL
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN 90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5052
Polymers24,0771
Non-polymers4271
Water4,017223
1
A: HEAT SHOCK PROTEIN 90
hetero molecules

A: HEAT SHOCK PROTEIN 90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0094
Polymers48,1552
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)73.910, 73.910, 110.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein HEAT SHOCK PROTEIN 90 / HSP90


Mass: 24077.387 Da / Num. of mol.: 1 / Fragment: N-TERMINAL
Source method: isolated from a genetically manipulated source
Details: ATP COMPLEX
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / References: UniProt: P02829
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growMethod: under oil / pH: 5
Details: PROTEIN WAS CRYSTALLIZED UNDER OIL IN TERASAKI PLATES. THE DROPS CONTAINED 27MG/ML PROTEIN, 9.75%(W/V) PEGME 550, 65MM AMMONIUM SULFATE, 32.5MM SODIUM SUCCINATE PH5.0, 5MM ATP AND 5MM ...Details: PROTEIN WAS CRYSTALLIZED UNDER OIL IN TERASAKI PLATES. THE DROPS CONTAINED 27MG/ML PROTEIN, 9.75%(W/V) PEGME 550, 65MM AMMONIUM SULFATE, 32.5MM SODIUM SUCCINATE PH5.0, 5MM ATP AND 5MM MAGNESIUM CHLORIDE., under oil
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
136 mg/mlprotein11
23 %mPEG55011
320 mM11CaCl2
410 mMTris-HCl11
55 mMnucleotide11
65 mM11Mg2+

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: TORROIDAL PT-COATED SI MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→24 Å / Num. obs: 21414 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.116 / Net I/σ(I): 3.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.24 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.116
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.24

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: PDB ENTRY 1AH6

1ah6


Resolution: 2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rwork0.189 ---
obs0.189 20586 97.7 %-
Rfree---RANDOM
Displacement parametersBiso mean: 23.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 27 223 1939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.98
X-RAY DIFFRACTIONx_mcangle_it2.86
X-RAY DIFFRACTIONx_scbond_it4.02
X-RAY DIFFRACTIONx_scangle_it6.04
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.238 3331 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2ADP.PARWATER.TOP
X-RAY DIFFRACTION3WATER.PARADP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68
LS refinement shell
*PLUS
Rfactor obs: 0.238

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