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Yorodumi- EMDB-40677: Structural insights into cellular control of the human CPEB3 prio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40677 | |||||||||||||||||||||
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Title | Structural insights into cellular control of the human CPEB3 prion, functionally regulated by a labile-amyloid-forming segment | |||||||||||||||||||||
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Sample |
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Keywords | prion / amyloid / reversible / helical / PROTEIN FIBRIL | |||||||||||||||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational elongation / : / CCR4-NOT complex / regulation of dendritic spine development / 3'-UTR-mediated mRNA destabilization / translation factor activity, RNA binding / apical dendrite / mRNA 3'-UTR AU-rich region binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of dendritic spine development ...negative regulation of cytoplasmic translational elongation / : / CCR4-NOT complex / regulation of dendritic spine development / 3'-UTR-mediated mRNA destabilization / translation factor activity, RNA binding / apical dendrite / mRNA 3'-UTR AU-rich region binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of dendritic spine development / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of cytoplasmic translation / long-term memory / mRNA regulatory element binding translation repressor activity / cellular response to amino acid stimulus / mRNA 3'-UTR binding / positive regulation of translation / regulation of synaptic plasticity / RNA stem-loop binding / ribosome binding / midbody / postsynaptic density / negative regulation of translation / neuron projection / synapse / dendrite / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||||||||
Authors | Flores MD / Sawaya MR / Boyer DR / Zink S / Fioriti L / Rodriguez JA | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: To Be Published Title: Structure of a reversible amyloid fibril formed by the CPEB3 prion-like domain reveals a core sequence involved in translational regulation Authors: Flores MD / Sawaya MR / Boyer DR / Zink S / Fioriti L / Rodriguez JA | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40677.map.gz | 11.4 MB | EMDB map data format | |
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Header (meta data) | emd-40677-v30.xml emd-40677.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40677_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_40677.png | 29.9 KB | ||
Filedesc metadata | emd-40677.cif.gz | 5.6 KB | ||
Others | emd_40677_half_map_1.map.gz emd_40677_half_map_2.map.gz | 171.4 MB 171.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40677 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40677 | HTTPS FTP |
-Validation report
Summary document | emd_40677_validation.pdf.gz | 668.8 KB | Display | EMDB validaton report |
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Full document | emd_40677_full_validation.pdf.gz | 668.4 KB | Display | |
Data in XML | emd_40677_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | emd_40677_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40677 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40677 | HTTPS FTP |
-Related structure data
Related structure data | 8spaMC 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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-Map
File | Download / File: emd_40677.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_40677_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40677_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Helical assembly of CPEB3 prion-like domain 1
Entire | Name: Helical assembly of CPEB3 prion-like domain 1 |
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Components |
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-Supramolecule #1: Helical assembly of CPEB3 prion-like domain 1
Supramolecule | Name: Helical assembly of CPEB3 prion-like domain 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Truncated CPEB3 prion-like domain generated recombinantly |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23 kDa/nm |
-Macromolecule #1: Cytoplasmic polyadenylation element-binding protein 3
Macromolecule | Name: Cytoplasmic polyadenylation element-binding protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 5.279761 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: LSPSFGSTWS TGTTNAVEDS FFQGITPVNG TMLFQNFPHH VNPVFGGTF UniProtKB: Cytoplasmic polyadenylation element-binding protein 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |