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- PDB-8k2t: Solution structure of full-length HtpG in complex with D131D -

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Basic information

Entry
Database: PDB / ID: 8k2t
TitleSolution structure of full-length HtpG in complex with D131D
Components
  • Chaperone protein HtpG
  • Nuclease A
KeywordsCHAPERONE / HtpG / E coli Hsp90
Function / homology
Function and homology information


micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / ATP-dependent protein folding chaperone / unfolded protein binding / nucleic acid binding / ATP hydrolysis activity / extracellular region / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. ...Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / 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 ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chaperone protein HtpG / Thermonuclease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Staphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsQu, X. / Huang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770807 31971144 China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Structural basis for the dynamic chaperoning of disordered clients by Hsp90.
Authors: Qu, X. / Zhao, S. / Wan, C. / Zhu, L. / Ji, T. / Rossi, P. / Wang, J. / Kalodimos, C.G. / Wang, C. / Xu, W. / Huang, C.
History
DepositionJul 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 30, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein HtpG
B: Chaperone protein HtpG
C: Nuclease A


Theoretical massNumber of molelcules
Total (without water)158,0723
Polymers158,0723
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chaperone protein HtpG


Mass: 71519.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: htpG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C3TLA7
#2: Protein Nuclease A


Mass: 15033.458 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00644
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HN(CO)CA
161isotropic13D HNCO
171isotropic13D 1H-13C NOESY
181isotropic13D 1H-15N NOESY
191isotropic23D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 500 uM [U-13C; U-15N; U-2H] Heat shock protein 90(HtpG M domain), 500 uM [U-2H, 15N; Ala- 13CH3; Met- 13CH3; Ile-d1- 13CH3; Leu, Val- 13CH3/ 13CH3; Thr- 13CH3] Heat shock protein 90(HtpG M ...Contents: 500 uM [U-13C; U-15N; U-2H] Heat shock protein 90(HtpG M domain), 500 uM [U-2H, 15N; Ala- 13CH3; Met- 13CH3; Ile-d1- 13CH3; Leu, Val- 13CH3/ 13CH3; Thr- 13CH3] Heat shock protein 90(HtpG M domian), 500 uM [U-13C; U-15N; U-2H] Heat shock protein 90(HtpG N domain), 500 uM [U-100% 13C; U-100% 15N] Disordered protein(D131D), 500 uM [U-2H, 15N; Ala- 13CH3; Met- 13CH3; Ile-d1- 13CH3; Leu, Val- 13CH3/ 13CH3; Thr- 13CH3] Heat shock protein 90(HtpG N domain), 600 uM [U-2H, 15N; Ala- 13CH3; Met- 13CH3; Ile-d1- 13CH3; Leu, Val- 13CH3/ 13CH3; Thr- 13CH3] Heat shock protein 90(HtpG C domain), 500 uM [U-2H, 15N; Ala- 13CH3; Met- 13CH3; Ile-d1- 13CH3; Leu, Val- 13CH3/ 13CH3; Thr- 13CH3] Heat shock protein 90(HtpG-D131D), 500 uM [U-2H, 15N; Ala- 13CH3; Met- 13CH3; Ile-d1- 13CH3; Leu, Val- 13CH3/ 13CH3; Thr- 13CH3] Heat shock protein 90(HtpG M-D131D N), 500 uM [U-2H, 15N; Ala- 13CH3; Met- 13CH3; Ile-d1- 13CH3; Leu, Val- 13CH3/ 13CH3; Thr- 13CH3] Heat shock protein 90(HtpG M-D131D C), 93% H2O/7% D2O
Label: 13C_samples / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMHeat shock protein 90(HtpG M domain)[U-13C; U-15N; U-2H]1
500 uMHeat shock protein 90(HtpG M domian)[U-2H, 15N; Ala- 13CH3; Met- 13CH3; Ile-d1- 13CH3; Leu, Val- 13CH3/ 13CH3; Thr- 13CH3]1
500 uMDisordered protein(D131D)[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 150 mM / Label: condition1 / pH: 7 / Pressure: 1 Pa / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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