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- PDB-8spa: Structural insights into cellular control of the human CPEB3 prio... -

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Basic information

Entry
Database: PDB / ID: 8spa
TitleStructural insights into cellular control of the human CPEB3 prion, functionally regulated by a labile-amyloid-forming segment
ComponentsCytoplasmic polyadenylation element-binding protein 3
KeywordsPROTEIN FIBRIL / prion / amyloid / reversible / helical
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 nuclear-transcribed mRNA poly(A) tail shortening / 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 nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of dendritic spine development / long-term memory / negative regulation of cytoplasmic translation / mRNA regulatory element binding translation repressor activity / positive regulation of translation / mRNA 3'-UTR binding / cellular response to amino acid stimulus / regulation of synaptic plasticity / RNA stem-loop binding / ribosome binding / midbody / neuron projection / negative regulation of translation / postsynaptic density / synapse / dendrite / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cytoplasmic polyadenylation element-binding protein, ZZ domain / Cytoplasmic polyadenylation element-binding protein / CEBP, ZZ domain superfamily / Cytoplasmic polyadenylation element-binding protein ZZ domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Cytoplasmic polyadenylation element-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsFlores, M.D. / Sawaya, M.R. / Boyer, D.R. / Zink, S. / Fioriti, L. / Rodriguez, J.A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128867 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM1295410 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007185 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
The Pew Charitable TrustsJAR United States
David and Lucile Packard FoundationJAR United States
CitationJournal: 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
DepositionMay 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytoplasmic polyadenylation element-binding protein 3
B: Cytoplasmic polyadenylation element-binding protein 3
C: Cytoplasmic polyadenylation element-binding protein 3
D: Cytoplasmic polyadenylation element-binding protein 3
E: Cytoplasmic polyadenylation element-binding protein 3


Theoretical massNumber of molelcules
Total (without water)26,3995
Polymers26,3995
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical 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
Cytoplasmic polyadenylation element-binding protein 3 / CPE-BP3 / CPE-binding protein 3 / hCPEB-3


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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical assembly of CPEB3 prion-like domain 1 / Type: COMPLEX
Details: Truncated CPEB3 prion-like domain generated recombinantly
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 23 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 5
Buffer component
IDConc.NameFormulaBuffer-ID
1125 mMsodium chlorideNaCl1
250 mMTris-Base1
310 mMdipotassium phosphateHK2PO41
45 mMglutamic acid1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2EPU2.8image acquisition
4RELION3CTF correction
8PHENIXmodel refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.32 ° / Axial rise/subunit: 4.81 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40329 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0061940
ELECTRON MICROSCOPYf_angle_d0.7532655
ELECTRON MICROSCOPYf_dihedral_angle_d10.816620
ELECTRON MICROSCOPYf_chiral_restr0.045285
ELECTRON MICROSCOPYf_plane_restr0.005350

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