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- EMDB-54295: Egalitarian-BicD in complex with K10 TLS RNA (Structure D) -

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Basic information

Entry
Database: EMDB / ID: EMD-54295
TitleEgalitarian-BicD in complex with K10 TLS RNA (Structure D)
Map data
Sample
  • Complex: Egalitarian-BicD in complex with K10 TLS RNA
    • Protein or peptide: Protein bicaudal D
    • Protein or peptide: Egalitarian, isoform B
    • RNA: TLS
KeywordsComplex / Transport / Localization / RNA BINDING PROTEIN
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
Protein bicaudal D / Egalitarian, isoform B
Similarity search - Component
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_54295.png

Downloads & links

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Map

FileDownload / File: emd_54295.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.16 Å		1.06 Å/pix.
x 240 pix.
= 254.16 Å		1.06 Å/pix.
x 240 pix.
= 254.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.038080055 - 0.07321695
Average (Standard dev.)0.0000024601818 (±0.0017627326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_54295_additional_1.map
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Half map: #1

Fileemd_54295_half_map_1.map
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Half map: #2

Fileemd_54295_half_map_2.map
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Sample components

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Entire : Egalitarian-BicD in complex with K10 TLS RNA

EntireName: Egalitarian-BicD in complex with K10 TLS RNA
Components
  • Complex: Egalitarian-BicD in complex with K10 TLS RNA
    • Protein or peptide: Protein bicaudal D
    • Protein or peptide: Egalitarian, isoform B
    • RNA: TLS

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Supramolecule #1: Egalitarian-BicD in complex with K10 TLS RNA

SupramoleculeName: Egalitarian-BicD in complex with K10 TLS RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Egalitarian-BicD in complex with the transport and localization signal (TLS) of the Drosophila fs(1)K10 mRNA
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Protein bicaudal D

MacromoleculeName: Protein bicaudal D / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 89.073547 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSASNNGPS ADQSVQDLQM EVERLTRELD QVSSASAQSA QYGLSLLEEK SALQQKCEEL ETLYDNTRHE LDITQEALTK FQTSQKVTN KTGIEQEDAL LNESAARETS LNLQIFDLEN ELKQLRHELE RVRNERDRML QENSDFGRDK SDSEADRLRL K SELKDLKF ...String:
MSSASNNGPS ADQSVQDLQM EVERLTRELD QVSSASAQSA QYGLSLLEEK SALQQKCEEL ETLYDNTRHE LDITQEALTK FQTSQKVTN KTGIEQEDAL LNESAARETS LNLQIFDLEN ELKQLRHELE RVRNERDRML QENSDFGRDK SDSEADRLRL K SELKDLKF RETRMLSEYS ELEEENISLQ KQVSSLRSSQ VEFEGAKHEI RRLTEEVELL NQQVDELANL KKIAEKQMEE AL ETLQGER EAKYALKKEL DGHLNRESMY HISNLAYSIR SNMEDNASNN SDGEEENLAL KRLEADLSTE LKSPDGTKCD LFS EIHLNE LKKLEKQLES MESEKTHLTA NLREAQTSLD KSQNELQNFM SRLALLAAHV DALVQLKKQI DVKEQGKEGG QKKD ELEQQ LRALISQYAN WFTLSAKEID GLKTDIAELQ KGLNYTDATT TLRNEVTNLK NKLLATEQKS LDLQSDVQTL THISQ NAGQ SLGSARSTLV ALSDDLAQLY HLVCTVNGET PTRVLLDHKT DDMSFENDSL TAIQSQFKSD VFIAKPQIVE DLQGLA DSV EIKKYVDTVS DQIKYLKTAV EHTIDMNKHK IRSEGGDALE KVNTEEMEEL QEQIVKLKSL LSVKREQIGT LRNVLKS NK QTAEVALTNL KSKYENEKII VSDTMSKLRN ELRLLKEDAA TFSSLRAMFA ARCEEYVTQV DDLNRQLEAA EEEKKTLN Q LLRLAVQQKL ALTQRLEEME MDREMRHVRR PMPAQRGTSG KSSFSTRPSS RNPASSNANP F

UniProtKB: Protein bicaudal D

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Macromolecule #2: Egalitarian, isoform B

MacromoleculeName: Egalitarian, isoform B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 113.198102 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MESMEYEMAR NMTLLFFLER LLDKGEPRTV HDLSCQFGNK EFTKEMRQIA GGSQSGLKKF LAQYPAIFLV DGDYVQVNAY QHHNADDGG CGGKRDYIQE AKDYFKNKML QYGAAAEVPV RSLLGHRSQA SPQVRHISGQ HIKEFTDFLM KHTDTFKVTD D YVMLVGCE ...String:
MESMEYEMAR NMTLLFFLER LLDKGEPRTV HDLSCQFGNK EFTKEMRQIA GGSQSGLKKF LAQYPAIFLV DGDYVQVNAY QHHNADDGG CGGKRDYIQE AKDYFKNKML QYGAAAEVPV RSLLGHRSQA SPQVRHISGQ HIKEFTDFLM KHTDTFKVTD D YVMLVGCE NMTDLPARDR LHLPQSNIDT RGTQQMLDFF AQCIEVKGPL LVDQLFHLLT TNFPQDQWLR MFKTPGDLSS FL KLFADCF HIQANLVTLL QKPKLSDTHI QQAQAQTREQ FNALNNNNSA SIRKQEPTPG GGGVGGVSSV QQRLQSPALR TNG HTNNNN GSNGSNNNNN NNNSIACPNF KLNAPVSNVM GGQSQGFGQP KSEPSSGFDS YVPMSELKLE NLCENNYPSA NTCY GPINN SSQQTQQVQT QQQQQPQHAT QNPAEQRLNS VNQTLKQRIN TLVIRTLAEN LEKDKQSLAN QQGGPISPHA SPVHS IANS SSNQNAGSAA NNANSNSNAN PNNANHSPSH SYFVGDTWKI KVLQNTTVIA NVKQSVFVTD IILKYAAKNE SIVVSL DCE GINLGLKGEI TLIEIGTTRG EAFLFDVQSC PAMVTDGGLK TVLEHDQVIK VIHDCRNDAA NLYLQFGILL RNVFDTQ AA HAILQYQESG KQVYKAKYIS LNSLCEQYNA PCNPIKDQLK QIYRRDQKFW AKRPLTREMM LYAAGDVLVL IHDQLFGN L ARQIKPENRA LFSELCTEQI LMQIKPNEVK IRKKQRKVST EVSDLKQKLA QTSKSIVLSN REIRLLRYMD LTEDEKERL KGYYKVAKKL EKMESAGNPS KDQSDSEDEQ EPNENDAFPS LDSVPSDNSL SGTFSPRFSS EPPSLTESMQ MLEEILQNKS MDRIARIDK LEAILTTATS LPCEQIIASN SMQEQLGSSI ATTENLQIIR EKSKNIKNCN CQGERSVTPI MRTTDKRVVK L VDAESQTL STGDVVITKI FFQDEHERAK EAALLSNSPA KRVSPTGSEN LYFQ

UniProtKB: Egalitarian, isoform B

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Macromolecule #3: TLS

MacromoleculeName: TLS / type: rna / ID: 3 / Number of copies: 2
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 18.962188 KDa
SequenceString:
UUACACCACU UGAUUGUAUU UUUAAAUUAA UUCUUAAAAA CUACAAAUUA AGAUCACUCU

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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: 76319
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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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: Predicted models used for all components
Output model

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

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