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- PDB-6cjs: Candida albicans Hsp90 nucleotide binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6cjs
TitleCandida albicans Hsp90 nucleotide binding domain in complex with AUY922
ComponentsHeat shock protein 90 homologHeat shock response
KeywordsCHAPERONE / Hsp90. ATPase
Function / homology
Function and homology information


negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / hyphal cell wall / fungal-type cell wall / filamentous growth / intracellular steroid hormone receptor signaling pathway / ATP-dependent protein folding chaperone / extracellular vesicle / unfolded protein binding / protein folding ...negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / hyphal cell wall / fungal-type cell wall / filamentous growth / intracellular steroid hormone receptor signaling pathway / ATP-dependent protein folding chaperone / extracellular vesicle / unfolded protein binding / protein folding / cellular response to heat / regulation of apoptotic process / protein stabilization / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / 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-2GJ / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKirkpatrick, M.G. / Pizarro, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI120958 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for species-selective targeting of Hsp90 in a pathogenic fungus.
Authors: Whitesell, L. / Robbins, N. / Huang, D.S. / McLellan, C.A. / Shekhar-Guturja, T. / LeBlanc, E.V. / Nation, C.S. / Hui, R. / Hutchinson, A. / Collins, C. / Chatterjee, S. / Trilles, R. / Xie, ...Authors: Whitesell, L. / Robbins, N. / Huang, D.S. / McLellan, C.A. / Shekhar-Guturja, T. / LeBlanc, E.V. / Nation, C.S. / Hui, R. / Hutchinson, A. / Collins, C. / Chatterjee, S. / Trilles, R. / Xie, J.L. / Krysan, D.J. / Lindquist, S. / Porco Jr., J.A. / Tatu, U. / Brown, L.E. / Pizarro, J. / Cowen, L.E.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7363
Polymers26,2091
Non-polymers5282
Water2,720151
1
A: Heat shock protein 90 homolog
hetero molecules

A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4736
Polymers52,4172
Non-polymers1,0554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area4800 Å2
ΔGint-36 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.210, 86.210, 225.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-478-

HOH

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Components

#1: Protein Heat shock protein 90 homolog / Heat shock response


Mass: 26208.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876
Gene: HSP90, CAALFM_C702030WA, CaJ7.0234, CaO19.13868, CaO19.6515
Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta 2 / References: UniProt: P46598
#2: Chemical ChemComp-2GJ / 5-[2,4-DIHYDROXY-5-(1-METHYLETHYL)PHENYL]-N-ETHYL-4-[4-(MORPHOLIN-4-YLMETHYL)PHENYL]ISOXAZOLE-3-CARBOXAMIDE / Luminespib


Mass: 465.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H31N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 4 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes 0.02M MgCl2 22% Polyacrylic acid sodium salt 5100

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.89→43.1 Å / Num. obs: 34601 / % possible obs: 99.9 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3371 / % possible all: 99.6

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CJI

6cji


Resolution: 1.9→43.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 --Random selection and thin slices
Rwork0.1668 ---
obs-34578 99.95 %-
Refinement stepCycle: LAST / Resolution: 1.9→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 38 151 1924

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