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- PDB-8b7j: Human HSP90 alpha ATP Binding Domain, ATP-lid closed conformation... -

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Basic information

Entry
Database: PDB / ID: 8b7j
TitleHuman HSP90 alpha ATP Binding Domain, ATP-lid closed conformation, R46A
ComponentsHSP90AA1 protein
KeywordsCHAPERONE / Human Chaperone Protein / HSP90 alpha / N-Terminal Domain / ATP Binding Domain / Ground State / ATP-lid Closed State
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / myelin sheath / cellular response to heat / protein stabilization / neuronal cell body / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex ...ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / myelin sheath / cellular response to heat / protein stabilization / neuronal cell body / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / 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 ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsRioual, E. / Henot, F. / Favier, A. / Macek, P. / Crublet, E. / Josso, P. / Brustcher, B. / Frech, M. / Gans, P. / Loison, C. / Boisbouvier, J.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05-02 France
Citation
Journal: Nat Commun / Year: 2022
Title: Visualizing the transiently populated closed-state of human HSP90 ATP binding domain.
Authors: Henot, F. / Rioual, E. / Favier, A. / Macek, P. / Crublet, E. / Josso, P. / Brutscher, B. / Frech, M. / Gans, P. / Loison, C. / Boisbouvier, J.
#1: Journal: Biorxiv / Year: 2022
Title: Visualizing the Transiently Populated Closed-State of Human HSP90 ATP Binding Domain
Authors: Henot, F. / Rioual, E. / Favier, A. / Macek, P. / Crublet, E. / Josso, P. / Brutscher, B. / Frech, M. / Gans, P. / Loison, C. / Boisbouvier, J.
History
DepositionSep 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HSP90AA1 protein


Theoretical massNumber of molelcules
Total (without water)29,9341
Polymers29,9341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000target function
RepresentativeModel #1closest to the average

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Components

#1: Protein HSP90AA1 protein


Mass: 29934.477 Da / Num. of mol.: 1 / Mutation: R46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1 / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q2VPJ6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY
122isotropic23D HCC-COSY
131isotropic32D Methyl-TROSY
143isotropic33D HCC-COSY
152isotropic33D HC(C)C-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-15N; U-2H; 13C(1H)3 ALA-b, ILE-d1, LEU-d2, MET-e, THR-g, VAL-g2] HSP90 alpha NTD, 150 mM Na+, 150 mM Cl-, 1 mM TCEP, 20 mM [U-2H] HEPES, 100% D2OPerdeuterated and Specifically U-15N; U-2H; 13C(1H)3 ALA-b, ILE-d1, LEU-d2, MET-e, THR-g, VAL-g2 methyl groups[U-15N; U-2H; 13C(1H)3 ALA-b, ILE-d1, LEU-d2, MET-e, THR-g, VAL-g2]100% D2O
solution20.5 mM [U-15N; U-2H; LEU U-13C, U-2H, 13C(1H)3d2, 12C(2H)3d1; VAL U-13C, U-2H, 13C(1H)3g2, 12C(2H)3g1; ILE U-13C, U-2H, 13C(1H)3d1, 12C(2H)3g2] HSP90 alpha NTD, 150 mM Na+, 150 mM Cl-, 1 mM TCEP, 20 mM [U-2H] HEPES, 100% D2OPerdeuterated and Specifically 13C(1H)3 sample labelled ILE-d1, LEU-d2, VAL-g2 methyl groups[U-15N; U-2H; LEU U-13C, U-2H, 13C(1H)3d2, 12C(2H)3d1; VAL U-13C, U-2H, 13C(1H)3g2, 12C(2H)3g1; ILE U-13C, U-2H, 13C(1H)3d1, 12C(2H)3g2]100% D2O
solution30.5 mM [U-15N, THR U-13C, ALA U-13C] HSP90 alpha NTD, 150 mM Na+, 150 mM Cl-, 1 mM TCEP, 20 mM HEPES, 100% D2OPerdeuterated and Specifically THR, ALA methyl groups[U-15N, THR U-13C, ALA U-13C]100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHSP90 alpha NTD[U-15N; U-2H; 13C(1H)3 ALA-b, ILE-d1, LEU-d2, MET-e, THR-g, VAL-g2]1
150 mMNa+natural abundance1
150 mMCl-natural abundance1
1 mMTCEPnatural abundance1
20 mMHEPES[U-2H]1
0.5 mMHSP90 alpha NTD[U-15N; U-2H; LEU U-13C, U-2H, 13C(1H)3d2, 12C(2H)3d1; VAL U-13C, U-2H, 13C(1H)3g2, 12C(2H)3g1; ILE U-13C, U-2H, 13C(1H)3d1, 12C(2H)3g2]2
150 mMNa+natural abundance2
150 mMCl-natural abundance2
1 mMTCEPnatural abundance2
20 mMHEPES[U-2H]2
0.5 mMHSP90 alpha NTD[U-15N, THR U-13C, ALA U-13C]3
150 mMNa+natural abundance3
150 mMCl-natural abundance3
1 mMTCEPnatural abundance3
20 mMHEPESnatural abundance3
Sample conditionsIonic strength: 150 mM / Label: pH 7.5 / pH: 7.5 / Pressure: 1 bar / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD95015 mm Cryogenic Probes head
Bruker AVANCE III HDBrukerAVANCE III HD85025 mm Cryogenic Probes head
Bruker AVANCE III HDBrukerAVANCE III HD60035 mm Cryogenic Probes head

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.5.2CCPNchemical shift assignment
CcpNmr Analysis2.5.2CCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 20

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