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

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Basic information

Entry
Database: PDB / ID: 6cjp
TitleCandida albicans Hsp90 nucleotide binding domain in complex with radicicol
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-F5S / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNation, C. / 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
B: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3484
Polymers52,4172
Non-polymers9312
Water54030
1
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6742
Polymers26,2091
Non-polymers4651
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)26,6742
Polymers26,2091
Non-polymers4651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.530, 80.110, 78.200
Angle α, β, γ (deg.)90.000, 105.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


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-F5S / (1aR,2Z,4E,6E,14R,15aR)-9,11-dihydroxy-6-{[(4-methoxyphenyl)methoxy]imino}-14-methyl-1a,6,7,14,15,15a-hexahydro-12H-oxireno[e][2]benzoxacyclotetradecin-12-one


Mass: 465.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27NO7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM Hepes 5mM CoCl2 12% PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→55 Å / Num. obs: 14455 / % possible obs: 96.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 17
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1855 / % possible all: 86

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CJI

6cji


Resolution: 2.6→39.2 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.246 --
Rwork0.203 --
obs-14434 96.5 %
Refinement stepCycle: LAST / Resolution: 2.6→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 68 30 3201

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