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

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Basic information

Entry
Database: PDB / ID: 6cjr
TitleCandida albicans Hsp90 nucleotide binding domain in complex with SNX-2112
ComponentsHeat shock protein 90 homolog
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 / nuclear receptor-mediated steroid hormone signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / extracellular vesicle ...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 / nuclear receptor-mediated steroid hormone signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / extracellular vesicle / cellular response to heat / regulation of apoptotic process / protein stabilization / perinuclear region of cytoplasm / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Histidine kinase-like ATPase, C-terminal domain / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Histidine kinase-like ATPase, C-terminal domain / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E0G / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein 90 homolog
B: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9444
Polymers52,4172
Non-polymers5272
Water5,098283
1
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6732
Polymers26,2091
Non-polymers4641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2712
Polymers26,2091
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.633, 73.633, 109.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Heat shock protein 90 homolog


Mass: 26208.641 Da / Num. of mol.: 2
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-E0G / 4-[6,6-dimethyl-4-oxidanylidene-3-(trifluoromethyl)-5,7-dihydroindazol-1-yl]-2-[(4-oxidanylcyclohexyl)amino]benzamide


Mass: 464.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis-Tris 0.2M MgCl2 25% PEG 3350

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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: 1.79→50 Å / Num. obs: 53380 / % possible obs: 99.08 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.36
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 4969 / % possible all: 92.81

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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: 1.8→27.3 Å / Cross valid method: FREE R-VALUE / Details: Twin law=h,-k,-l (Twin fraction=0.20)
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 --Random selection and thin slices
Rwork0.1726 ---
obs-53380 99 %-
Refinement stepCycle: LAST / Resolution: 1.8→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 37 283 3647

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