[English] 日本語
Yorodumi- EMDB-26726: PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain he... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26726 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain hexamer bound to ATPgammaS, closed conformation | |||||||||||||||||||||
Map data | PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain hexamer bound to ATPgammaS in the closed conformation from 3DVA | |||||||||||||||||||||
Sample |
| |||||||||||||||||||||
Keywords | AAA+ ATPase / Chaperone / Mitochondria / Protein Folding | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||||||||
Authors | Gupta A / Lentzsch AM / Siegel AS / Yu Z / Lu C / Chio US / Cheng Y / Shan S | |||||||||||||||||||||
Funding support | United States, 6 items
| |||||||||||||||||||||
Citation | Journal: Sci Adv / Year: 2023 Title: Dodecamer assembly of a metazoan AAA chaperone couples substrate extraction to refolding. Authors: Arpit Gupta / Alfred M Lentzsch / Alex Siegel / Zanlin Yu / Un Seng Chio / Yifan Cheng / Shu-Ou Shan / Abstract: Ring-forming AAA chaperones solubilize protein aggregates and protect organisms from proteostatic stress. In metazoans, the AAA chaperone Skd3 in the mitochondrial intermembrane space (IMS) is ...Ring-forming AAA chaperones solubilize protein aggregates and protect organisms from proteostatic stress. In metazoans, the AAA chaperone Skd3 in the mitochondrial intermembrane space (IMS) is critical for human health and efficiently refolds aggregated proteins, but its underlying mechanism is poorly understood. Here, we show that Skd3 harbors both disaggregase and protein refolding activities enabled by distinct assembly states. High-resolution structures of Skd3 hexamers in distinct conformations capture ratchet-like motions that mediate substrate extraction. Unlike previously described disaggregases, Skd3 hexamers further assemble into dodecameric cages in which solubilized substrate proteins can attain near-native states. Skd3 mutants defective in dodecamer assembly retain disaggregase activity but are impaired in client refolding, linking the disaggregase and refolding activities to the hexameric and dodecameric states of Skd3, respectively. We suggest that Skd3 is a combined disaggregase and foldase, and this property is particularly suited to meet the complex proteostatic demands in the mitochondrial IMS. | |||||||||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_26726.map.gz | 108 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-26726-v30.xml emd-26726.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26726_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_26726.png | 68.6 KB | ||
Filedesc metadata | emd-26726.cif.gz | 5 KB | ||
Others | emd_26726_half_map_1.map.gz emd_26726_half_map_2.map.gz | 200.6 MB 200.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26726 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26726 | HTTPS FTP |
-Validation report
Summary document | emd_26726_validation.pdf.gz | 697.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_26726_full_validation.pdf.gz | 697.4 KB | Display | |
Data in XML | emd_26726_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | emd_26726_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26726 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26726 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_26726.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain hexamer bound to ATPgammaS in the closed conformation from 3DVA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0428 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain...
File | emd_26726_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain hexamer bound to ATPgammaS in the closed conformation, half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain...
File | emd_26726_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain hexamer bound to ATPgammaS in the closed conformation, half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : PARL-cleaved Skd3
Entire | Name: PARL-cleaved Skd3 |
---|---|
Components |
|
-Supramolecule #1: PARL-cleaved Skd3
Supramolecule | Name: PARL-cleaved Skd3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 397 KDa |
-Macromolecule #1: PARL-cleaved Skd3
Macromolecule | Name: PARL-cleaved Skd3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: YSKSPSNKDA ALLEAARANN MQEVSRLLSE GADVNAKHRL GWTALMVAAI NRNNSVVQVL LAAGADPNLG DDFSSVYKTA KEQGIHSLED GGQDGASRHI TNQWTSALEF RRWLGLPAGV LITREDDFNN RLNNRASFKG CTALHYAVLA DDYRTVKELL DGGANPLQRN ...String: YSKSPSNKDA ALLEAARANN MQEVSRLLSE GADVNAKHRL GWTALMVAAI NRNNSVVQVL LAAGADPNLG DDFSSVYKTA KEQGIHSLED GGQDGASRHI TNQWTSALEF RRWLGLPAGV LITREDDFNN RLNNRASFKG CTALHYAVLA DDYRTVKELL DGGANPLQRN EMGHTPLDYA REGEVMKLLR TSEAKYQEKQ RKREAEERRR FPLEQRLKEH IIGQESAIAT VGAAIRRKEN GWYDEEHPLV FLFLGSSGIG KTELAKQTAK YMHKDAKKGF IRLDMSEFQE RHEVAKFIGS PPGYVGHEEG GQLTKKLKQC PNAVVLFDQV DKAHPDVLTI MLQLFDEGRL TDGKGKTIDC KDAIFIMTSN VASDEIAQHA LQLRQEALEM SRNRIAENLG DVQISDKITI SKNFKENVIR PILKAHFRRD EFLGRINEIV YFLPFCHSEL IQLVNKELNF WAKRAKQRHN ITLLWDREVA DVLVDGYNVH YGARSIKHEV ERRVVNQLAA AYEQDLLPGG CTLRITVEDS DKQLLKSPEL PSPQAEKRLP KLRLEIIDKD SKTRRLDIRA PLHPEKVCNT I |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
---|---|
Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |