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- PDB-5zui: Crystal Structure of HSP104 from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 5zui
TitleCrystal Structure of HSP104 from Chaetomium thermophilum
ComponentsHeat Shock Protein 104Heat shock response
KeywordsCHAPERONE / PROTEIN DISAGGREGASE / ATPASE / TWO-RING AAA PROTEIN / HELICAL FILAMENT
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 profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily ...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 profile. / Clp, repeat (R) domain / 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
ADENOSINE-5'-DIPHOSPHATE / Putative heat shock protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsHanazono, Y. / Inoue, Y. / Noguchi, K. / Yohda, M. / Shinohara, K. / Takeda, K. / Miki, K.
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
DepositionMay 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 22, 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 104
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4879
Polymers85,0561
Non-polymers1,4318
Water905
1
A: Heat Shock Protein 104
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)518,92154
Polymers510,3366
Non-polymers8,58548
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation6_555x-y,x,z+5/61
Unit cell
Length a, b, c (Å)131.182, 131.182, 137.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Heat Shock Protein 104 / Heat shock response


Mass: 85056.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0022720 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S4G4*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence was deposited with accession number LC388394 to DDBJ.

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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: 4 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01 M Cobalt chloride, 0.1 M MES (pH6.5), 1.8 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 36348 / % possible obs: 99.1 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rsym value: 0.096 / Net I/σ(I): 31.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.591 / Rsym value: 1.268 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CIU

4ciu


Resolution: 2.701→47.382 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.65
RfactorNum. reflection% reflection
Rfree0.265 1828 5.04 %
Rwork0.2113 --
obs0.214 36292 98.84 %
Refinement stepCycle: LAST / Resolution: 2.701→47.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5399 0 84 5 5488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d
X-RAY DIFFRACTIONf_angle_d0.777477
X-RAY DIFFRACTIONf_dihedral_angle_d24.4232170
X-RAY DIFFRACTIONf_chiral_restr0.045857
X-RAY DIFFRACTIONf_plane_restr0.004963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7013-2.77430.50371150.39072407X-RAY DIFFRACTION89
2.7743-2.8560.40381380.32712579X-RAY DIFFRACTION96
2.856-2.94810.34291360.2922679X-RAY DIFFRACTION100
2.9481-3.05350.35471300.28552671X-RAY DIFFRACTION100
3.0535-3.17570.31461460.27362662X-RAY DIFFRACTION100
3.1757-3.32020.38691460.25912669X-RAY DIFFRACTION100
3.3202-3.49520.32961600.23252660X-RAY DIFFRACTION100
3.4952-3.71410.27651450.21392678X-RAY DIFFRACTION100
3.7141-4.00070.24851330.20612694X-RAY DIFFRACTION100
4.0007-4.40310.24851430.17822675X-RAY DIFFRACTION100
4.4031-5.03960.22751460.17452672X-RAY DIFFRACTION100
5.0396-6.3470.2991410.2252702X-RAY DIFFRACTION100
6.347-47.38910.18551490.17122716X-RAY DIFFRACTION100

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