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- EMDB-40677: Structural insights into cellular control of the human CPEB3 prio... -

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Basic information

Entry
Database: EMDB / ID: EMD-40677
TitleStructural insights into cellular control of the human CPEB3 prion, functionally regulated by a labile-amyloid-forming segment
Map data
Sample
  • Complex: Helical assembly of CPEB3 prion-like domain 1
    • Protein or peptide: Cytoplasmic polyadenylation element-binding protein 3
Keywordsprion / 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 / 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
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFlores MD / Sawaya MR / Boyer DR / Zink S / Fioriti L / Rodriguez JA
Funding support United States, 6 items
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 MD / Sawaya MR / Boyer DR / Zink S / Fioriti L / Rodriguez JA
History
DepositionMay 2, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40677.png

Downloads & links

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Map

FileDownload / File: emd_40677.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.0278
Minimum - Maximum-0.02719959 - 0.054891244
Average (Standard dev.)0.0001902964 (±0.0018641136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40677_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40677_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical assembly of CPEB3 prion-like domain 1

EntireName: Helical assembly of CPEB3 prion-like domain 1
Components
  • Complex: Helical assembly of CPEB3 prion-like domain 1
    • Protein or peptide: Cytoplasmic polyadenylation element-binding protein 3

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Supramolecule #1: Helical assembly of CPEB3 prion-like domain 1

SupramoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23 kDa/nm

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Macromolecule #1: Cytoplasmic polyadenylation element-binding protein 3

MacromoleculeName: Cytoplasmic polyadenylation element-binding protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.279761 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
LSPSFGSTWS TGTTNAVEDS FFQGITPVNG TMLFQNFPHH VNPVFGGTF

UniProtKB: Cytoplasmic polyadenylation element-binding protein 3

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 5
Component:
ConcentrationFormulaName
125.0 mMNaClsodium chloride
50.0 mMTris-Base
10.0 mMHK2PO4dipotassium phosphate
5.0 mMglutamic acid
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.81 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.32 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 40329
Startup modelType of model: OTHER / Details: ab initio model
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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