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Yorodumi- PDB-8spa: Structural insights into cellular control of the human CPEB3 prio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8spa | |||||||||||||||||||||
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Title | Structural insights into cellular control of the human CPEB3 prion, functionally regulated by a labile-amyloid-forming segment | |||||||||||||||||||||
Components | Cytoplasmic polyadenylation element-binding protein 3 | |||||||||||||||||||||
Keywords | PROTEIN FIBRIL / prion / amyloid / reversible / helical | |||||||||||||||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational elongation / CCR4-NOT complex / messenger ribonucleoprotein complex / regulation of dendritic spine development / translation factor activity, RNA binding / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / apical dendrite / 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 / messenger ribonucleoprotein complex / regulation of dendritic spine development / translation factor activity, RNA binding / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / apical dendrite / 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 / RNA stem-loop binding / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / positive regulation of translation / cellular response to amino acid stimulus / regulation of synaptic plasticity / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å | |||||||||||||||||||||
Authors | Flores, M.D. / Sawaya, M.R. / Boyer, D.R. / Zink, S. / Fioriti, L. / Rodriguez, J.A. | |||||||||||||||||||||
Funding support | United States, 6items
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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, M.D. / Sawaya, M.R. / Boyer, D.R. / Zink, S. / Fioriti, L. / Rodriguez, J.A. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8spa.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8spa.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 8spa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/8spa ftp://data.pdbj.org/pub/pdb/validation_reports/sp/8spa | HTTPS FTP |
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-Related structure data
Related structure data | 40677MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 5 / Rise per n subunits: 4.81 Å / Rotation per n subunits: -3.32 °) |
-Components
#1: Protein/peptide | Mass: 5279.761 Da / Num. of mol.: 5 / Fragment: PRD1 (UNP residues 103-151) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPEB3, KIAA0940 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8NE35 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Helical assembly of CPEB3 prion-like domain 1 / Type: COMPLEX Details: Truncated CPEB3 prion-like domain generated recombinantly Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 23 kDa/nm / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -3.32 ° / Axial rise/subunit: 4.81 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40329 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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