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- EMDB-39095: Funes-induced Orb2 amyloid like endogenous Orb2 amyloid -

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Basic information

Entry
Database: EMDB / ID: EMD-39095
TitleFunes-induced Orb2 amyloid like endogenous Orb2 amyloid
Map data
Sample
  • Complex: Funes-induced Orb2 amyloid filament
    • Protein or peptide: Translational regulator orb2
KeywordsTranslator regulator / chaperone / PROTEIN FIBRIL
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHervas R / Si K
Funding support United States, Hong Kong, 2 items
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 KKS / Mukhi M / Khaki S / Hervas R / Si K
History
DepositionFeb 8, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39095.png

Downloads & links

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Map

FileDownload / File: emd_39095.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 220 pix.
= 238.48 Å		1.08 Å/pix.
x 220 pix.
= 238.48 Å		1.08 Å/pix.
x 220 pix.
= 238.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0124
Minimum - Maximum-0.036233496 - 0.052395366
Average (Standard dev.)0.00020234015 (±0.0033360315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 238.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39095_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39095_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 : Funes-induced Orb2 amyloid filament

EntireName: Funes-induced Orb2 amyloid filament
Components
  • Complex: Funes-induced Orb2 amyloid filament
    • Protein or peptide: Translational regulator orb2

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Supramolecule #1: Funes-induced Orb2 amyloid filament

SupramoleculeName: Funes-induced Orb2 amyloid filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Translational regulator orb2

MacromoleculeName: Translational regulator orb2 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 3.97417 KDa
SequenceString:
QLHQQQHQQQ HQQHQQHQQQ QQLHQHQQQL S

UniProtKB: Translational regulator orb2

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.15
Details: 10 mM HEPES pH7.15, 75 mM NaCl, 10 mM KCl, 2mM MgCl2 and 5 mM TCEP
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsOrb2 amyloid induced by the JDP Funes from oligomeric Orb2 isolte from fly heads

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.82 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.42 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 7807
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

39095

Final angle assignmentType: NOT APPLICABLE

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