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- PDB-2xx4: Macrolactone Inhibitor bound to HSP90 N-term -

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Basic information

Entry
Database: PDB / ID: 2xx4
TitleMacrolactone Inhibitor bound to HSP90 N-term
ComponentsATP-DEPENDENT MOLECULAR CHAPERONE HSP82
KeywordsCHAPERONE
Function / homology
Function and homology information


The NLRP3 inflammasome / 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 / HSF1 activation / response to oxygen levels ...The NLRP3 inflammasome / 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 / 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 / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / 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
Chem-13I / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsMoody, C.J. / Prodromou, C. / Pearl, L.H. / Roe, S.M.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Targeting the Hsp90 Molecular Chaperone with Novel Macrolactams. Synthesis, Structural, Binding, and Cellular Studies.
Authors: Day, J.E. / Sharp, S.Y. / Rowlands, M.G. / Aherne, W. / Hayes, A. / Raynaud, F.I. / Lewis, W. / Roe, S.M. / Prodromou, C. / Pearl, L.H. / Workman, P. / Moody, C.J.
History
DepositionNov 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 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)24,6202
Polymers24,2091
Non-polymers4121
Water2,558142
1
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules

A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2414
Polymers48,4172
Non-polymers8242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area1980 Å2
ΔGint-6.1 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.736, 73.736, 110.000
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-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: Chemical ChemComp-13I / (E)-ETHYL 13-CHLORO-14,16-DIHYDROXY-1,11-DIOXO-1,2,3,4,7,8,9,10,11,12-DECAHYDROBENZO[C][1]AZACYCLOTETRADECINE-10-CARBOXYLATE


Mass: 411.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26ClNO6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.02 Å3/Da / Density % sol: 59.3 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER / Detector: CCD / Date: Dec 3, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 16082 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 27.04 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PROTEUM2data reduction
PROTEUM2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AH6

1ah6


Resolution: 2.199→32.831 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 799 5 %
Rwork0.2115 --
obs0.2146 16002 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.759 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.734 Å20 Å20 Å2
2---5.734 Å20 Å2
3---11.468 Å2
Refinement stepCycle: LAST / Resolution: 2.199→32.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 28 142 1836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071729
X-RAY DIFFRACTIONf_angle_d1.092337
X-RAY DIFFRACTIONf_dihedral_angle_d18.492659
X-RAY DIFFRACTIONf_chiral_restr0.072269
X-RAY DIFFRACTIONf_plane_restr0.007301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1986-2.33630.32271270.252467X-RAY DIFFRACTION100
2.3363-2.51670.34851280.24772478X-RAY DIFFRACTION100
2.5167-2.76980.32871690.23442475X-RAY DIFFRACTION100
2.7698-3.17030.2771350.22242508X-RAY DIFFRACTION100
3.1703-3.99320.27481400.19172532X-RAY DIFFRACTION99
3.9932-32.83510.20321000.18922743X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.4862 Å / Origin y: 5.5979 Å / Origin z: 1.0049 Å
111213212223313233
T0.0808 Å2-0.0013 Å2-0.0111 Å2-0.0895 Å20.0266 Å2--0.1317 Å2
L2.1091 °2-1.1256 °20.1366 °2-2.3867 °20.3414 °2--0.8863 °2
S-0.0188 Å °0.018 Å °0.4533 Å °0.0587 Å °-0.0679 Å °-0.5866 Å °-0.0151 Å °0.0058 Å °-0.0095 Å °
Refinement TLS groupSelection details: ALL

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