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- EMDB-54301: Egalitarian-BicD in complex with ILS of I-factor mRNA (Structure B) -

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Basic information

Entry
Database: EMDB / ID: EMD-54301
TitleEgalitarian-BicD in complex with ILS of I-factor mRNA (Structure B)
Map dataunsharpened map
Sample
  • Complex: Egalitarian-BicD in complex with ILS of I-factor mRNA
KeywordsComplex / Transport / Localization / RNA BINDING PROTEIN
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSingh K / Chilaeva S / McClintock MA / Bullock SL / Carter AP
Funding support United Kingdom, European Union, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 197-2021European Union
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Structural basis for recognition of diverse localizing mRNAs by Egl-BicD.
Authors: Kashish Singh / Sabila Chilaeva / Mark A McClintock / Andrew P Carter / Simon L Bullock /
Abstract: Localization of mRNAs is a widespread mechanism for dictating where proteins operate in cells and underpins many fundamental processes, from embryonic patterning to synaptic plasticity. This spatial ...Localization of mRNAs is a widespread mechanism for dictating where proteins operate in cells and underpins many fundamental processes, from embryonic patterning to synaptic plasticity. This spatial control is mediated by the interaction of 'localization signals' in target mRNAs with RNA-binding proteins (RBPs). These signals frequently lack overt sequence or structural patterns, raising the question of how specificity is achieved. Here we investigate this issue using the Drosophila RBP Egalitarian (Egl), which couples mRNAs to microtubule-based transport through Bicaudal D (BicD) and the dynein motor. We present cryo-electron microscopy structures of Egl-BicD bound to six different RNAs. Egl uses multiple noncanonical double-stranded RNA-binding domains to cooperatively form a recognition pocket around localization signals. Despite substantial variation in length and sequence, each signal adopts a bent stem-loop conformation that, together with base-pair identities at two defined sites, drives Egl engagement. We further demonstrate that Egl dimers couple RNA binding to transport initiation through coincident detection of two RNA elements within the same transcript. Thus, localizing mRNAs are recognized through a combination of shape, positional sequence features and number of structured RNA elements. This work reveals a molecular strategy by which diverse mRNAs can be selectively engaged by a single RBP.
History
DepositionJul 9, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54301.png

Downloads & links

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Map

FileDownload / File: emd_54301.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.24 Å		1.06 Å/pix.
x 360 pix.
= 381.24 Å		1.06 Å/pix.
x 360 pix.
= 381.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0664
Minimum - Maximum-0.1391637 - 0.56186867
Average (Standard dev.)0.0000046435366 (±0.008950084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_54301_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_54301_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54301_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Egalitarian-BicD in complex with ILS of I-factor mRNA

EntireName: Egalitarian-BicD in complex with ILS of I-factor mRNA
Components
  • Complex: Egalitarian-BicD in complex with ILS of I-factor mRNA

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Supramolecule #1: Egalitarian-BicD in complex with ILS of I-factor mRNA

SupramoleculeName: Egalitarian-BicD in complex with ILS of I-factor mRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Egalitarian-BicD in complex with I-factor localization signal (ILS) of I-factor retrotransposon mRNA
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
Details: 25 mM HEPES pH 7.3, 150 mM KCl, 1 mM MgCl2, 1mM DTT, 0.00125% IGEPAL
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio model was generated in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 154880
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4) / Details: Cryosparc
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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