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- PDB-4ce3: Hsp90 N-terminal domain bound to macrolactam analogues of radicicol. -

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Basic information

Entry
Database: PDB / ID: 4ce3
TitleHsp90 N-terminal domain bound to macrolactam analogues of radicicol.
ComponentsATP-DEPENDENT MOLECULAR CHAPERONE HSP82
KeywordsCHAPERONE
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 / HSF1-dependent transactivation / 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 / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion / regulation of telomere maintenance / box C/D snoRNP assembly / 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 / disordered domain specific binding / 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
Chem-L4V / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsRoe, S.M. / Parry-Morris, S. / Prodromou, C.
CitationJournal: Org.Biomol.Chem. / Year: 2014
Title: Synthesis of Macrolactam Analogues of Radicicol and Their Binding to Heat Shock Protein Hsp90.
Authors: Dutton, B.L. / Kitson, R.R.A. / Parry-Morris, S. / Roe, S.M. / Prodromou, C. / Moody, C.J.
History
DepositionNov 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5602
Polymers24,2091
Non-polymers3521
Water2,810156
1
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules

A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1214
Polymers48,4172
Non-polymers7042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area1870 Å2
ΔGint-10.8 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.180, 74.180, 110.490
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 ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 / 82 KDA HEAT SHOCK PROTEIN / HEAT SHOCK PROTEIN HSP90 HEAT-INDUCIBLE ISOFORM / HSP90


Mass: 24208.582 Da / Num. of mol.: 1 / Fragment: N-TERMINUS, 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: Chemical ChemComp-L4V / 13-Chloro-14,16-dihydroxy-2-methyl-2,3,4,5,9,10-hexahydrobenz[c][1]azacyclotetradecine-1,11(8H,12H)-dione


Mass: 351.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22ClNO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.17 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97961
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 2.31→52.45 Å / Num. obs: 13834 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 47.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.5
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AH6

1ah6


Resolution: 2.31→52.45 Å / Cor.coef. Fo:Fc: 0.9382 / Cor.coef. Fo:Fc free: 0.9104 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.275 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.202
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 692 5 %RANDOM
Rwork0.1959 ---
obs0.198 13833 97.82 %-
Displacement parametersBiso mean: 43.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.9172 Å20 Å20 Å2
2--2.9172 Å20 Å2
3----5.8344 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.31→52.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 24 156 1851
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011725HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.122333HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d828SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes259HARMONIC5
X-RAY DIFFRACTIONt_it1725HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion2.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion234SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2117SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.5 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2452 145 5.35 %
Rwork0.211 2563 -
all0.2129 2708 -
obs--97.82 %

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