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- PDB-2ygf: L89V, L93I and V136M Mutant of N-Term HSP90 complexed with Geldan... -

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Basic information

Entry
Database: PDB / ID: 2ygf
TitleL89V, L93I and V136M Mutant of N-Term HSP90 complexed with Geldanamycin
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
GELDANAMYCIN / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRoe, M. / Prodromou, C. / Pearl, L.H.
CitationJournal: Faseb J. / Year: 2011
Title: Features of the Streptomyces Hygroscopicus Htpg Reveal How Partial Geldanamycin Resistance Can Arise by Mutation to the ATP Binding Pocket of a Eukaryotic Hsp90.
Authors: Millson, S.H. / Chua, C.S. / Solovieva, S. / Roe, M. / Polier, S. / Pearl, L.H. / Sim, T.S. / Prodromou, C. / Piper, P.W.
History
DepositionApr 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other
Revision 1.2Feb 6, 2013Group: Atomic model
Revision 2.0Jun 28, 2017Group: Advisory / Atomic model / Data collection / Category: atom_site / database_PDB_caveat / diffrn_source
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,5443
Polymers24,8911
Non-polymers6532
Water2,666148
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.121, 74.121, 110.433
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: 24891.438 Da / Num. of mol.: 1 / Fragment: N-TERMINUS, RESIDUES 1-220 / Mutation: YES
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-GDM / GELDANAMYCIN / Geldanamycin


Mass: 560.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O9 / Comment: antitumor, antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 89 TO VAL ENGINEERED RESIDUE IN CHAIN A, LEU 93 TO ILE ...ENGINEERED RESIDUE IN CHAIN A, LEU 89 TO VAL ENGINEERED RESIDUE IN CHAIN A, LEU 93 TO ILE ENGINEERED RESIDUE IN CHAIN A, VAL 136 TO MET
Nonpolymer detailsGELDANAMYCIN (GDM) IS AN INHIBITOR OF HSP90 ORIGINALLY ISOLATED FROM STREPTOMYCES HYGROSCOPICUS (TAXID: 1912).

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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: 3.14 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→74.12 Å / Num. obs: 21531 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 43.3 % / Biso Wilson estimate: 36.22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 28.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE MODEL

Resolution: 2→25.872 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1099 5.1 %
Rwork0.2139 --
obs0.2164 21456 99.89 %
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.882 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.6713 Å20 Å20 Å2
2---4.6713 Å20 Å2
3---9.3426 Å2
Refinement stepCycle: LAST / Resolution: 2→25.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 46 148 1879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071766
X-RAY DIFFRACTIONf_angle_d1.0892384
X-RAY DIFFRACTIONf_dihedral_angle_d14.744671
X-RAY DIFFRACTIONf_chiral_restr0.068277
X-RAY DIFFRACTIONf_plane_restr0.004303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.30631490.25872474X-RAY DIFFRACTION100
2.091-2.20120.281310.23462489X-RAY DIFFRACTION100
2.2012-2.3390.27091500.22522487X-RAY DIFFRACTION100
2.339-2.51950.32061440.24862502X-RAY DIFFRACTION100
2.5195-2.77270.36221420.26912514X-RAY DIFFRACTION100
2.7727-3.17330.27421250.24632560X-RAY DIFFRACTION100
3.1733-3.99570.26041320.20792583X-RAY DIFFRACTION100
3.9957-25.8740.21351260.1772748X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.8384 Å / Origin y: -30.8533 Å / Origin z: 0.7498 Å
111213212223313233
T0.2213 Å20.0111 Å20.0238 Å2-0.2291 Å2-0.0099 Å2--0.1833 Å2
L2.9391 °2-0.7369 °2-0.2482 °2-1.5112 °20.0174 °2--1.1578 °2
S-0.0905 Å °-0.0147 Å °-0.0873 Å °0.0945 Å °0.0287 Å °0.0125 Å °-0.0621 Å °0.0117 Å °0.0548 Å °
Refinement TLS groupSelection details: CHAIN A

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