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Yorodumi- EMDB-33104: Structure and mechanism of a mitochondrial AAA+ disaggregase CLPB -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33104 | |||||||||
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Title | Structure and mechanism of a mitochondrial AAA+ disaggregase CLPB | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CLPB / AAA-ATPase / CHAPERONE | |||||||||
Function / homology | Function and homology information granulocyte differentiation / RIG-I signaling pathway / ATP-dependent protein disaggregase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / antiviral innate immune response / mitochondrial intermembrane space / cellular response to heat / ATP hydrolysis activity / mitochondrion / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.7 Å | |||||||||
Authors | Wu D / Liu Y / Dai Y / Wang G / Lu G / Chen Y / Li N / Lin J / Gao N | |||||||||
Funding support | China, 2 items
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Citation | Journal: PLoS Biol / Year: 2023 Title: Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization. Authors: Damu Wu / Yan Liu / Yuhao Dai / Guopeng Wang / Guoliang Lu / Yan Chen / Ningning Li / Jinzhong Lin / Ning Gao / Abstract: The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of- ...The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of-function CLPB mutations are associated with a few human diseases with neutropenia and neurological disorders. Unlike canonical AAA+ proteins, CLPB contains a unique ankyrin repeat domain (ANK) at its N-terminus. How CLPB functions as a disaggregase and the role of its ANK domain are currently unclear. Herein, we report a comprehensive structural characterization of human CLPB in both the apo- and substrate-bound states. CLPB assembles into homo-tetradecamers in apo-state and is remodeled into homo-dodecamers upon substrate binding. Conserved pore-loops (PLs) on the ATPase domains form a spiral staircase to grip and translocate the substrate in a step-size of 2 amino acid residues. The ANK domain is not only responsible for maintaining the higher-order assembly but also essential for the disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with a variety of mitochondrial substrates. These results reveal unique properties of CLPB as a general disaggregase in mitochondria and highlight its potential as a target for the treatment of various mitochondria-related diseases. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33104.map.gz | 59.1 MB | EMDB map data format | |
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Header (meta data) | emd-33104-v30.xml emd-33104.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_33104.png | 55.7 KB | ||
Filedesc metadata | emd-33104.cif.gz | 5.9 KB | ||
Others | emd_33104_half_map_1.map.gz emd_33104_half_map_2.map.gz | 52.1 MB 52.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33104 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33104 | HTTPS FTP |
-Related structure data
Related structure data | 7xbkMC 7xc5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33104.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33104_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33104_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CLPB
Entire | Name: CLPB |
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Components |
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-Supramolecule #1: CLPB
Supramolecule | Name: CLPB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Isoform 2 of Caseinolytic peptidase B protein homolog
Macromolecule | Name: Isoform 2 of Caseinolytic peptidase B protein homolog / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 75.566336 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLGSLVLRRK ALAPRLLLRL LRSPTLRGHG GASGRNVTTG SLGEPQWLRV ATGGRPGTSP ALFSGRGAAT GGRQGGRFDT KCLAAATWG RLPGPEETLP GQDSWNGVPS RAGLGMCALA AALVVHCYSK SPSNKDAALL EAARANNMQE VSRLLSEGAD V NAKHRLGW ...String: MLGSLVLRRK ALAPRLLLRL LRSPTLRGHG GASGRNVTTG SLGEPQWLRV ATGGRPGTSP ALFSGRGAAT GGRQGGRFDT KCLAAATWG RLPGPEETLP GQDSWNGVPS RAGLGMCALA AALVVHCYSK SPSNKDAALL EAARANNMQE VSRLLSEGAD V NAKHRLGW TALMVAAINR NNSVVQVLLA AGADPNLGDD FSSVYKTAKE QGIHSLEVLI TREDDFNNRL NNRASFKGCT AL HYAVLAD DYRTVKELLD GGANPLQRNE MGHTPLDYAR EGEVMKLLRT SEAKYQEKQR KREAEERRRF PLEQRLKEHI IGQ ESAIAT VGAAIRRKEN GWYDEEHPLV FLFLGSSGIG KTELAKQTAK YMHKDAKKGF IRLDMSEFQE RHEVAKFIGS PPGY VGHEE GGQLTKKLKQ CPNAVVLFDQ VDKAHPDVLT IMLQLFDEGR LTDGKGKTID CKDAIFIMTS NVASDEIAQH ALQLR QEAL EMSRNRIAEN LGDVQISDKI TISKNFKENV IRPILKAHFR RDEFLGRINE IVYFLPFCHS ELIQLVNKEL NFWAKR AKQ RHNITLLWDR EVADVLVDGY NVHYGARSIK HEVERRVVNQ LAAAYEQDLL PGGCTLRITV EDSDKQLLKS PELPSPQ AE KRLPKLRLEI IDKDSKTRRL DIRAPLHPEK VCNTI UniProtKB: Mitochondrial disaggregase |
-Macromolecule #2: Unknown peptide
Macromolecule | Name: Unknown peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.464797 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 6.8 |
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Staining | Type: NEGATIVE / Material: Uranyl Acetare |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45907 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |