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- EMDB-54306: Egalitarian-BicD in complex with hSL1 and hSL2 of the hairy local... -

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Basic information

Entry
Database: EMDB / ID: EMD-54306
TitleEgalitarian-BicD in complex with hSL1 and hSL2 of the hairy localization element
Map data
Sample
  • Complex: Egalitarian-BicD in complex with hSL1 and hSL2 of the hairy localization element
    • Protein or peptide: Protein bicaudal D
    • Protein or peptide: Egalitarian, isoform B
    • RNA: hairy localization element
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 / 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 ...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 / 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 / cargo adaptor activity / COPI-independent Golgi-to-ER retrograde traffic / positive regulation of clathrin-dependent endocytosis / chaeta development / transport along microtubule / RNA transport / oocyte axis specification / clathrin heavy chain binding / cytoskeletal anchor activity / intracellular mRNA localization / nucleobase-containing compound metabolic process / oogenesis / regulation of endocytosis / dynein complex binding / dynactin binding / mRNA transport / synaptic vesicle endocytosis / 3'-5' exonuclease activity / regulation of microtubule cytoskeleton organization / small GTPase binding / presynapse / cytoskeleton / mRNA binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
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: 3.4 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: To Be Published
Title: Structures of Egl-BicD reveal how diverse mRNAs are selected for subcellular localization
Authors: Singh K / Chilaeva S / McClintock MA / Bullock SL / Carter AP
History
DepositionJul 9, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54306.png

Downloads & links

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Map

FileDownload / File: emd_54306.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 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

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.1991396 - 2.0871785
Average (Standard dev.)0.00033932654 (±0.035060663)
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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Mask #1

Fileemd_54306_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_54306_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_54306_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_54306_half_map_2.map
Projections & Slices
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Sample components

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Entire : Egalitarian-BicD in complex with hSL1 and hSL2 of the hairy local...

EntireName: Egalitarian-BicD in complex with hSL1 and hSL2 of the hairy localization element
Components
  • Complex: Egalitarian-BicD in complex with hSL1 and hSL2 of the hairy localization element
    • Protein or peptide: Protein bicaudal D
    • Protein or peptide: Egalitarian, isoform B
    • RNA: hairy localization element

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Supramolecule #1: Egalitarian-BicD in complex with hSL1 and hSL2 of the hairy local...

SupramoleculeName: Egalitarian-BicD in complex with hSL1 and hSL2 of the hairy localization element
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Egalitarian-BicD in complex with stem loop 1 (hSL1) and stem loop 2 (hSL2) of the hairy localization element
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: hairy localization element

MacromoleculeName: hairy localization element / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 48.400551 KDa
SequenceString:
GCGCAUGCGC GUAGACAUUU CACAUCAUUC GCCGGGAUUG CGCAAAUGUU GCUUUGAAGU GUUGCAAACA UGCGAAUCCU AAACUCGGU UCACAACUUC GUUGGCUUAG UUUCCUGGCU UAUAUCCUGG AAACCCGUCG ACGAGGCUAA GG

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 202684
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-9rwb:
Egalitarian-BicD in complex with hSL1 and hSL2 of the hairy localization element

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