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- PDB-8spa: Structural insights into cellular control of the human CPEB3 prio... -
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Open data
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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 | |||||||||||||||||||||
![]() | Cytoplasmic polyadenylation element-binding protein 3 | |||||||||||||||||||||
![]() | PROTEIN FIBRIL / prion / amyloid / reversible / helical | |||||||||||||||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational elongation / : / CCR4-NOT 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 / 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 / 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 / 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 | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å | |||||||||||||||||||||
![]() | Flores, M.D. / Sawaya, M.R. / Boyer, D.R. / Zink, S. / Fioriti, L. / Rodriguez, J.A. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.9 KB | Display | ![]() |
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PDB format | ![]() | 35.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 970 KB | Display | ![]() |
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Full document | ![]() | 970.5 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 40677MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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 °) |
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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.) ![]() Production host: ![]() ![]() 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 |
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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: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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 |
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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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