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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 / neuron projection / negative regulation of translation / protein stabilization / postsynapse / 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: Proc Natl Acad Sci U S A / Year: 2026
Title: A J-domain protein enhances memory by promoting physiological amyloid formation in .
Authors: Kyle Patton / Yangyang Yi / Raj Burt / Kevin Kan-Shing Ng / Mayur Mukhi / Peerzada Shariq Shaheen Khaki / Ruben Hervas / Kausik Si /
Abstract: Memory requires experience-dependent alterations in the synaptic proteome. Chaperones interface between the environment and the proteome. Manipulating J-domain protein (JDP) chaperones, the most ...Memory requires experience-dependent alterations in the synaptic proteome. Chaperones interface between the environment and the proteome. Manipulating J-domain protein (JDP) chaperones, the most diverse family of chaperones, in a neuronal circuit that encodes associative long-term memories, we identified yet uncharacterized JDPs that transduce sensory cues. One of these JDPs, CG10375, which we named Funes, enhances memory when overexpressed and impairs memory when functionally impaired. Funes overexpression enhances memory formation even when sensory stimuli are suboptimal. At the circuit level, Funes acts on neurons where conditioned and unconditioned stimuli converge to form associative memories. From a proteomic-based screen, we found that overexpression of Funes changes the solubility of a small subset of proteins, one of which is the mRNA-binding protein Orb2. Combining in vitro and in vivo biophysical, biochemical, and cryo-EM structural analyses, we found that Funes associates with oligomeric Orb2 and promotes the formation of translationally active amyloids. Perturbation of the conserved J domain eliminates the ability of Funes to facilitate amyloid assembly and promote memory. We posit that the brain harbors chaperones that influence memory by regulating physiological amyloid formation.
History
DepositionFeb 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: 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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