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Yorodumi- EMDB-30349: Staggered ring conformation of CtHsp104 (Hsp104 from Chaetomium T... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30349 | |||||||||||||||
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Title | Staggered ring conformation of CtHsp104 (Hsp104 from Chaetomium Thermophilum) | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | AAA+ ATPase / disaggregation / CHAPERONE | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Chaetomium thermophilum (fungus) / Chaetomium thermophilum var. coprophilum (fungus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 Å | |||||||||||||||
Authors | Inoue Y / Hanazono Y | |||||||||||||||
Funding support | Japan, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30349.map.gz | 12.2 MB | EMDB map data format | |
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Header (meta data) | emd-30349-v30.xml emd-30349.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
Images | emd_30349.png | 102.3 KB | ||
Masks | emd_30349_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-30349.cif.gz | 6.3 KB | ||
Others | emd_30349_half_map_1.map.gz emd_30349_half_map_2.map.gz | 71.1 MB 71.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30349 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30349 | HTTPS FTP |
-Related structure data
Related structure data | 7cg3MC 5zuiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30349.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_30349_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30349_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_30349_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : a spiral hexamer ring structure of Hsp104
Entire | Name: a spiral hexamer ring structure of Hsp104 |
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Components |
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-Supramolecule #1: a spiral hexamer ring structure of Hsp104
Supramolecule | Name: a spiral hexamer ring structure of Hsp104 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
-Macromolecule #1: Heat shock protein 104
Macromolecule | Name: Heat shock protein 104 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum var. coprophilum (fungus) |
Molecular weight | Theoretical: 85.05607 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVDSRNADTE QENENLSKFC IDMTAMAREG KIDPVIGREE EIRRVIRILS RRTKNNPVLI GEPGVGKTTI VEGLAQRIVN ADVPDNLAA CKLLSLDVGA LVAGSKYRGE FEERMKGVLK EIQESKETII LFVDEIHLLM GAGSSGEGGM DAANLLKPML A RGQLHCIG ...String: MVDSRNADTE QENENLSKFC IDMTAMAREG KIDPVIGREE EIRRVIRILS RRTKNNPVLI GEPGVGKTTI VEGLAQRIVN ADVPDNLAA CKLLSLDVGA LVAGSKYRGE FEERMKGVLK EIQESKETII LFVDEIHLLM GAGSSGEGGM DAANLLKPML A RGQLHCIG ATTLAEYRKY IEKDAAFERR FQQVLVKEPS ITETISILRG LKEKYEVHHG VNIADAAIVA AANLAARYLT SR RLPDSAV DLIDEAAAAV RVARESQPEI IDSLERRLRQ LKIEIHALSR EKDEASKARL AQAKQDAQNV EEELRPLREK YER ERQRGK AIQEAKMKLE ALRVKAEDAS RMGDHSRAAD LQYYAIPEQE AIIKRLEAEK AAADAALNAN GADVGGSMIT DVVG PDQIN EIVARWTGIP VTRLKTSEKE KLLHMEQALS KIVVGQKEAV QSVSNAIRLQ RSGLSNPNQP PSFLFCGPSG TGKTL LTKA LAEFLFDDPK SMIRFDMSEY QERHSLSRMI GAPPGYVGHD AGGQLTEALR RRPFSILLFD EVEKAAKEVL TVLLQL MDD GRITDGQGRV VDAKNCIVVM TSNLGAEYLS RANNGKDGKI DPTTRELVMN TLRNYFLPEF LNRISSIVIF NRLTRRE IR KIVDLRIAEI QKRLTDNDRN VTIKVSDEAK DKLGAQGYSP VYGARPLQRL LEKEVLNRLA ILILRGQIRE GEVACVEL V DGKVQVLPNH PDSEPEDVDV DMESDDAVDE VAPDSMDEDI YND UniProtKB: Heat shock protein 104 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Microscope was modified with a Cs corrector |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 4198 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |