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- PDB-7cg3: Staggered ring conformation of CtHsp104 (Hsp104 from Chaetomium T... -

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Basic information

Entry
Database: PDB / ID: 7cg3
TitleStaggered ring conformation of CtHsp104 (Hsp104 from Chaetomium Thermophilum)
ComponentsHeat shock protein 104
KeywordsCHAPERONE / AAA+ ATPase / disaggregation
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. ...ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Heat shock protein 104
Similarity search - Component
Biological speciesChaetomium thermophilum var. coprophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsInoue, Y. / Hanazono, Y. / Noi, K. / Kawamoto, A. / Kimatsuka, M. / Harada, R. / Takeda, K. / Iwamasa, N. / Shibata, K. / Noguchi, K. ...Inoue, Y. / Hanazono, Y. / Noi, K. / Kawamoto, A. / Kimatsuka, M. / Harada, R. / Takeda, K. / Iwamasa, N. / Shibata, K. / Noguchi, K. / Shigeta, Y. / Namba, K. / Ogura, T. / Miki, K. / Shinohara, K. / Yohda, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)P15J08261 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04572 Japan
Japan Society for the Promotion of Science (JSPS)JP16H00753 Japan
Japan Society for the Promotion of Science (JSPS)18H04690 Japan
CitationJournal: Structure / Year: 2021
Title: Split conformation of Chaetomium thermophilum Hsp104 disaggregase.
Authors: Yosuke Inoue / Yuya Hanazono / Kentaro Noi / Akihiro Kawamoto / Masato Kimatsuka / Ryuhei Harada / Kazuki Takeda / Ryoichi Kita / Natsuki Iwamasa / Kyoka Shibata / Keiichi Noguchi / Yasuteru ...Authors: Yosuke Inoue / Yuya Hanazono / Kentaro Noi / Akihiro Kawamoto / Masato Kimatsuka / Ryuhei Harada / Kazuki Takeda / Ryoichi Kita / Natsuki Iwamasa / Kyoka Shibata / Keiichi Noguchi / Yasuteru Shigeta / Keiichi Namba / Teru Ogura / Kunio Miki / Kyosuke Shinohara / Masafumi Yohda /
Abstract: Hsp104 and its bacterial homolog ClpB form hexameric ring structures and mediate protein disaggregation. The disaggregated polypeptide is thought to thread through the central channel of the ring. ...Hsp104 and its bacterial homolog ClpB form hexameric ring structures and mediate protein disaggregation. The disaggregated polypeptide is thought to thread through the central channel of the ring. However, the dynamic behavior of Hsp104 during disaggregation remains unclear. Here, we reported the stochastic conformational dynamics and a split conformation of Hsp104 disaggregase from Chaetomium thermophilum (CtHsp104) in the presence of ADP by X-ray crystallography, cryo-electron microscopy (EM), and high-speed atomic force microscopy (AFM). ADP-bound CtHsp104 assembles into a 6 left-handed spiral filament in the crystal structure at a resolution of 2.7 Å. The unit of the filament is a hexamer of the split spiral structure. In the cryo-EM images, staggered and split hexameric rings were observed. Further, high-speed AFM observations showed that a substrate addition enhanced the conformational change and increased the split structure's frequency. Our data suggest that split conformation is an off-pathway state of CtHsp104 during disaggregation.
History
DepositionJun 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 29, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
F: Heat shock protein 104
A: Heat shock protein 104
B: Heat shock protein 104
C: Heat shock protein 104
D: Heat shock protein 104
E: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)510,3366
Polymers510,3366
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Heat shock protein 104


Mass: 85056.070 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. coprophilum (fungus)
Gene: hsp104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2Z6G185

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: a spiral hexamer ring structure of Hsp104 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 4198
EM imaging opticsSpherical aberration corrector: Microscope was modified with a Cs corrector

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1738736
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180636 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 203 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5ZUI

5zui


Accession code: 5ZUI / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00429867
ELECTRON MICROSCOPYf_angle_d0.69940218
ELECTRON MICROSCOPYf_dihedral_angle_d12.1024136
ELECTRON MICROSCOPYf_chiral_restr0.0454683
ELECTRON MICROSCOPYf_plane_restr0.0055234

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