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Yorodumi- EMDB-21316: Cryo-EM structure of the amyloid core of Drosophila Orb2 isolated... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21316 | |||||||||
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Title | Cryo-EM structure of the amyloid core of Drosophila Orb2 isolated from head | |||||||||
Map data | amyloid core of Drosophila Orb2 isolated from head | |||||||||
Sample |
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Keywords | amyloid / prion-like / long-term memory / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information dendrite terminus / sperm axoneme assembly / male courtship behavior / asymmetric cell division / sperm individualization / translation activator activity / messenger ribonucleoprotein complex / translation factor activity, RNA binding / male meiosis I / long-term memory ...dendrite terminus / sperm axoneme assembly / male courtship behavior / asymmetric cell division / sperm individualization / translation activator activity / messenger ribonucleoprotein complex / translation factor activity, RNA binding / male meiosis I / long-term memory / negative regulation of cytoplasmic translation / axon terminus / mRNA regulatory element binding translation repressor activity / positive regulation of translation / synaptic membrane / mRNA 3'-UTR binding / ribosome binding / presynapse / cell body / cell cortex / perikaryon / postsynapse / spermatogenesis / negative regulation of translation / protein stabilization / neuron projection / axon / synapse / perinuclear region of cytoplasm / protein-containing complex / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Hervas R / Rau MJ | |||||||||
Citation | Journal: Science / Year: 2020 Title: Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in . Authors: Ruben Hervas / Michael J Rau / Younshim Park / Wenjuan Zhang / Alexey G Murzin / James A J Fitzpatrick / Sjors H W Scheres / Kausik Si / Abstract: How long-lived memories withstand molecular turnover is a fundamental question. Aggregates of a prion-like RNA-binding protein, cytoplasmic polyadenylation element-binding (CPEB) protein, is a ...How long-lived memories withstand molecular turnover is a fundamental question. Aggregates of a prion-like RNA-binding protein, cytoplasmic polyadenylation element-binding (CPEB) protein, is a putative substrate of long-lasting memories. We isolated aggregated CPEB, Orb2, from adult heads and determined its activity and atomic structure, at 2.6-angstrom resolution, using cryo-electron microscopy. Orb2 formed ~75-nanometer-long threefold-symmetric amyloid filaments. Filament formation transformed Orb2 from a translation repressor to an activator and "seed" for further translationally active aggregation. The 31-amino acid protofilament core adopted a cross-β unit with a single hydrophilic hairpin stabilized through interdigitated glutamine packing. Unlike the hydrophobic core of pathogenic amyloids, the hydrophilic core of Orb2 filaments suggests how some neuronal amyloids could be a stable yet regulatable substrate of memory. | |||||||||
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_21316.map.gz | 9 MB | EMDB map data format | |
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Header (meta data) | emd-21316-v30.xml emd-21316.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21316_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_21316.png | 69.7 KB | ||
Masks | emd_21316_msk_1.map | 40.6 MB | Mask map | |
Filedesc metadata | emd-21316.cif.gz | 4.3 KB | ||
Others | emd_21316_half_map_1.map.gz emd_21316_half_map_2.map.gz | 31.2 MB 31.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21316 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21316 | HTTPS FTP |
-Related structure data
Related structure data | 6vpsMC 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_21316.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | amyloid core of Drosophila Orb2 isolated from head | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 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_21316_msk_1.map | ||||||||||||
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Density Histograms |
-Half map: half map 1
File | emd_21316_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
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Density Histograms |
-Half map: half map 2
File | emd_21316_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : amyloid core of Drosophila Orb2
Entire | Name: amyloid core of Drosophila Orb2 |
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Components |
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-Supramolecule #1: amyloid core of Drosophila Orb2
Supramolecule | Name: amyloid core of Drosophila Orb2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) / Tissue: head |
-Macromolecule #1: Translational regulator orb2
Macromolecule | Name: Translational regulator orb2 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 3.97417 KDa |
Sequence | String: QLHQQQHQQQ HQQHQQHQQQ QQLHQHQQQL S UniProtKB: Translational regulator orb2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.25 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 63.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |