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Yorodumi- EMDB-3095: Electron negative stain tomography of alpha-synuclein amyloid fib... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3095 | |||||||||
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Title | Electron negative stain tomography of alpha-synuclein amyloid fibrils treated with the Hsc70/DNAJB1/Apg2 chaperone system | |||||||||
Map data | Reconstruction of alpha-synuclein amyloid fibrils treated with the Hsc70/DNAJB1/Apg2 trichaperone system | |||||||||
Sample |
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Keywords | alpha-synuclein amyloid fibrils / disaggregation activity | |||||||||
Function / homology | Function and homology information negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / regulation of norepinephrine uptake / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dopamine uptake involved in synaptic transmission / dynein complex binding / regulation of dopamine secretion / positive regulation of receptor recycling / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / supramolecular fiber organization / axon terminus / mitochondrial ATP synthesis coupled electron transport / inclusion body / fatty acid metabolic process / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / adult locomotory behavior / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / synapse organization / microglial cell activation / negative regulation of protein kinase activity / regulation of long-term neuronal synaptic plasticity / protein destabilization / ferrous iron binding / tau protein binding / positive regulation of protein serine/threonine kinase activity / PKR-mediated signaling / receptor internalization / phospholipid binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / synaptic vesicle membrane / positive regulation of inflammatory response / positive regulation of peptidyl-serine phosphorylation / actin cytoskeleton / actin binding / cellular response to oxidative stress / histone binding / cell cortex / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / transcription cis-regulatory region binding / postsynapse / amyloid fibril formation / response to lipopolysaccharide / molecular adaptor activity / oxidoreductase activity / lysosome / response to xenobiotic stimulus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / negative staining | |||||||||
Authors | Gao X / Carroni M / Nussbaum-Krammer C / Mogk A / Nillegoda NB / Szlachcic A / Guilbride DL / Saibil HR / Mayer MP / Bukau B | |||||||||
Citation | Journal: Mol Cell / Year: 2015 Title: Human Hsp70 Disaggregase Reverses Parkinson's-Linked α-Synuclein Amyloid Fibrils. Authors: Xuechao Gao / Marta Carroni / Carmen Nussbaum-Krammer / Axel Mogk / Nadinath B Nillegoda / Anna Szlachcic / D Lys Guilbride / Helen R Saibil / Matthias P Mayer / Bernd Bukau / Abstract: Intracellular amyloid fibrils linked to neurodegenerative disease typically accumulate in an age-related manner, suggesting inherent cellular capacity for counteracting amyloid formation in early ...Intracellular amyloid fibrils linked to neurodegenerative disease typically accumulate in an age-related manner, suggesting inherent cellular capacity for counteracting amyloid formation in early life. Metazoan molecular chaperones assist native folding and block polymerization of amyloidogenic proteins, preempting amyloid fibril formation. Chaperone capacity for amyloid disassembly, however, is unclear. Here, we show that a specific combination of human Hsp70 disaggregase-associated chaperone components efficiently disassembles α-synuclein amyloid fibrils characteristic of Parkinson's disease in vitro. Specifically, the Hsc70 chaperone, the class B J-protein DNAJB1, and an Hsp110 family nucleotide exchange factor (NEF) provide ATP-dependent activity that disassembles amyloids within minutes via combined fibril fragmentation and depolymerization. This ultimately generates non-toxic α-synuclein monomers. Concerted, rapid interaction cycles of all three chaperone components with fibrils generate the power stroke required for disassembly. This identifies a powerful human Hsp70 disaggregase activity that efficiently disassembles amyloid fibrils and points to crucial yet undefined biology underlying amyloid-based diseases. | |||||||||
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_3095.map.gz | 2.4 GB | EMDB map data format | |
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Header (meta data) | emd-3095-v30.xml emd-3095.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | EMD-3095.png | 4.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3095 | HTTPS FTP |
-Validation report
Summary document | emd_3095_validation.pdf.gz | 128.3 KB | Display | EMDB validaton report |
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Full document | emd_3095_full_validation.pdf.gz | 127.4 KB | Display | |
Data in XML | emd_3095_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3095 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3095 | HTTPS FTP |
-Related structure data
Related structure data | 3094C 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_3095.map.gz / Format: CCP4 / Size: 2.8 GB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of alpha-synuclein amyloid fibrils treated with the Hsc70/DNAJB1/Apg2 trichaperone system | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.028 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : alpha-synuclein fibrils plus chaperones Hsc70, DNAJB1 and Apg2
Entire | Name: alpha-synuclein fibrils plus chaperones Hsc70, DNAJB1 and Apg2 |
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Components |
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-Supramolecule #1000: alpha-synuclein fibrils plus chaperones Hsc70, DNAJB1 and Apg2
Supramolecule | Name: alpha-synuclein fibrils plus chaperones Hsc70, DNAJB1 and Apg2 type: sample / ID: 1000 / Number unique components: 4 |
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-Macromolecule #1: alpha-synuclein
Macromolecule | Name: alpha-synuclein / type: protein_or_peptide / ID: 1 / Oligomeric state: amyloid fibrils / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 14 KDa / Theoretical: 14 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pTYB11 |
Sequence | UniProtKB: Alpha-synuclein |
-Macromolecule #2: Hsc70
Macromolecule | Name: Hsc70 / type: protein_or_peptide / ID: 2 / Name.synonym: HSPA8 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 70 KDa / Theoretical: 70 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #3: DNAJB1
Macromolecule | Name: DNAJB1 / type: protein_or_peptide / ID: 3 / Name.synonym: Hdj1 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 40 KDa / Theoretical: 40 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #4: Apg2
Macromolecule | Name: Apg2 / type: protein_or_peptide / ID: 4 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 95 KDa / Theoretical: 95 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 50 mM Hepes-KOH pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT, 2 mM ATP, 3 mM PEP, 20 ng/microL pyruvate kinase |
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Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 2% w/v uranyl formate for 2 minutes |
Grid | Details: 200 mesh copper finder grids with thin carbon support glow discharged in atmosphere. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Dec 7, 2014 |
Image recording | Category: CCD / Film or detector model: OTHER / Average electron dose: 200 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 3 ° |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Software - Name: IMOD / Number images used: 40 |
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CTF correction | Details: IMOD |