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- PDB-8yac: Funes-induced Orb2 amyloid like endogenous Orb2 amyloid -

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Basic information

Entry
Database: PDB / ID: 8yac
TitleFunes-induced Orb2 amyloid like endogenous Orb2 amyloid
ComponentsTranslational regulator orb2
KeywordsPROTEIN FIBRIL / Translator regulator / chaperone
Function / homology
Function and homology information


dendrite terminus / sperm axoneme assembly / asymmetric cell division / sperm individualization / male courtship behavior / translation activator activity / translation factor activity, RNA binding / male meiosis I / long-term memory / negative regulation of cytoplasmic translation ...dendrite terminus / sperm axoneme assembly / asymmetric cell division / sperm individualization / male courtship behavior / translation activator activity / translation factor activity, RNA binding / male meiosis I / long-term memory / negative regulation of cytoplasmic translation / axon terminus / mRNA regulatory element binding translation repressor activity / synaptic membrane / positive regulation of translation / mRNA 3'-UTR binding / presynapse / ribosome binding / cell body / cell cortex / spermatogenesis / perikaryon / postsynapse / neuron projection / negative regulation of translation / protein stabilization / axon / synapse / perinuclear region of cytoplasm / protein-containing complex / RNA binding / identical protein binding / nucleus / 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
Translational regulator orb2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHervas, R. / Si, K.
Funding support United States, Hong Kong, 2items
OrganizationGrant numberCountry
Other private United States
Other government Hong Kong
CitationJournal: To Be Published
Title: J-domain protein Funes enhances memory by facilitating amyloid formation.
Authors: Patton, K. / Yi, Y. / Burt, R. / Ng, K.K.S. / Mukhi, M. / Khaki, S. / Hervas, R. / Si, K.
History
DepositionFeb 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translational regulator orb2
B: Translational regulator orb2
C: Translational regulator orb2
D: Translational regulator orb2
E: Translational regulator orb2
F: Translational regulator orb2
G: Translational regulator orb2
H: Translational regulator orb2
I: Translational regulator orb2


Theoretical massNumber of molelcules
Total (without water)35,7689
Polymers35,7689
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
Translational regulator orb2


Mass: 3974.170 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VSR3
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: Funes-induced Orb2 amyloid filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 7.15
Details: 10 mM HEPES pH7.15, 75 mM NaCl, 10 mM KCl, 2mM MgCl2 and 5 mM TCEP
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Orb2 amyloid induced by the JDP Funes from oligomeric Orb2 isolte from fly heads
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4GctfCTF correction
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.42 ° / Axial rise/subunit: 4.82 Å / Axial symmetry: C3
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7807 / Symmetry type: HELICAL

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