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- PDB-9rw1: Egalitarian-BicD in complex with K10 TLS RNA (Structure D) -

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Basic information

Entry
Database: PDB / ID: 9rw1
TitleEgalitarian-BicD in complex with K10 TLS RNA (Structure D)
Components
  • Egalitarian, isoform B
  • Protein bicaudal D
  • TLS
KeywordsRNA BINDING PROTEIN / Complex / Transport / Localization
Function / homology
Function and homology information


larval salivary gland morphogenesis / oocyte nucleus migration involved in oocyte dorsal/ventral axis specification / intracellular mRNA localization involved in pattern specification process / microtubule anchoring at microtubule organizing center / oocyte axis specification / germarium-derived egg chamber formation / bicoid mRNA localization / regulation of oskar mRNA translation / oocyte microtubule cytoskeleton polarization / oocyte microtubule cytoskeleton organization ...larval salivary gland morphogenesis / oocyte nucleus migration involved in oocyte dorsal/ventral axis specification / intracellular mRNA localization involved in pattern specification process / microtubule anchoring at microtubule organizing center / oocyte axis specification / germarium-derived egg chamber formation / bicoid mRNA localization / regulation of oskar mRNA translation / oocyte microtubule cytoskeleton polarization / oocyte microtubule cytoskeleton organization / germarium-derived oocyte fate determination / pole plasm oskar mRNA localization / positive regulation of synaptic vesicle exocytosis / protein transport along microtubule / COPI-independent Golgi-to-ER retrograde traffic / positive regulation of clathrin-dependent endocytosis / cargo adaptor activity / chaeta development / transport along microtubule / RNA transport / clathrin heavy chain binding / intracellular mRNA localization / cytoskeletal adaptor activity / mRNA transport / oogenesis / regulation of endocytosis / dynactin binding / dynein complex binding / synaptic vesicle endocytosis / 3'-5' exonuclease activity / regulation of microtubule cytoskeleton organization / small GTPase binding / presynapse / cytoskeleton / mRNA binding / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
: / Egalitarian winged helix domain / Bicaudal-D protein / Microtubule-associated protein Bicaudal-D / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein bicaudal D / Egalitarian, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSingh, K. / Chilaeva, S. / McClintock, M.A. / Bullock, S.L. / Carter, A.P.
Funding support United Kingdom, European Union, 2items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein bicaudal D
B: Protein bicaudal D
D: Egalitarian, isoform B
C: Egalitarian, isoform B
E: TLS
F: TLS


Theoretical massNumber of molelcules
Total (without water)442,4686
Polymers442,4686
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 Protein bicaudal D


Mass: 89073.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: BicD, CG6605 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P16568
#2: Protein Egalitarian, isoform B / Egalitarian / isoform C


Mass: 113198.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: egl, Dmel\CG4051, egal, EGL, Egl, CG4051, Dmel_CG4051 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9W1K4
#3: RNA chain TLS


Mass: 18962.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Egalitarian-BicD in complex with K10 TLS RNA / Type: COMPLEX
Details: Egalitarian-BicD in complex with the transport and localization signal (TLS) of the Drosophila fs(1)K10 mRNA
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera (butterflies/moths)
Buffer solutionpH: 7.3
Details: 25 mM HEPES pH 7.3, 150 mM KCl, 1 mM MgCl2, 1mM DTT, 0.00125% IGEPAL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraXmodel fitting
9PHENIX1.20_4459model refinement
10cryoSPARC4initial Euler assignment
11RELION5final Euler assignment
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76319 / Symmetry type: POINT
Atomic model buildingDetails: Predicted models used for all components / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310501
ELECTRON MICROSCOPYf_angle_d0.62314543
ELECTRON MICROSCOPYf_dihedral_angle_d10.5612171
ELECTRON MICROSCOPYf_chiral_restr0.0371712
ELECTRON MICROSCOPYf_plane_restr0.0041551

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