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- PDB-9ujy: The structure of Egalitarian in complex with the K10 mRNA localiz... -

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Basic information

Entry
Database: PDB / ID: 9ujy
TitleThe structure of Egalitarian in complex with the K10 mRNA localization signal reveals a modular binding surface required for function
ComponentsMaltose/maltodextrin-binding periplasmic protein,Egalitarian, isoform B
KeywordsRNA BINDING PROTEIN / RNA / localization / Drosophila / Egalitarian / CRISPR
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 / bicoid mRNA localization / regulation of oskar mRNA translation / oocyte microtubule cytoskeleton organization / germarium-derived oocyte fate determination / pole plasm oskar mRNA localization / transport along microtubule / intracellular mRNA localization ...larval salivary gland morphogenesis / oocyte nucleus migration involved in oocyte dorsal/ventral axis specification / intracellular mRNA localization involved in pattern specification process / bicoid mRNA localization / regulation of oskar mRNA translation / oocyte microtubule cytoskeleton organization / germarium-derived oocyte fate determination / pole plasm oskar mRNA localization / transport along microtubule / intracellular mRNA localization / nucleobase-containing compound metabolic process / oogenesis / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / mRNA transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 3'-5' exonuclease activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / mRNA binding / DNA damage response / membrane / metal ion binding
Similarity search - Function
: / Egalitarian winged helix domain / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein ...: / Egalitarian winged helix domain / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Egalitarian, isoform B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsHong, Z. / Muehle, J. / Bono, F.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)FP7/2007-2013European Union
CitationJournal: Biorxiv / Year: 2026
Title: The structure of Egalitarian in complex with the K10 mRNA localization signal reveals a modular binding surface required for function
Authors: Hong, Z. / Jin, L. / Muhle, J. / Bono, F.
History
DepositionApr 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Egalitarian, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5312
Polymers47,1891
Non-polymers3421
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint7 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.001, 82.311, 120.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Egalitarian, isoform B / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Egalitarian / isoform C


Mass: 47188.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: malE, b4034, JW3994, egl, Dmel\CG4051, egal, EGL, Egl, CG4051, Dmel_CG4051
Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q9W1K4
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 100 mM Tris-HCl, pH 7.5, 18% (w/v) PEG 6000, 50 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 50894 / % possible obs: 99.2 % / Redundancy: 3.08 % / Biso Wilson estimate: 50.53 Å2 / CC1/2: 0.996 / Net I/σ(I): 0.12
Reflection shellResolution: 2.2→2.34 Å / Num. unique obs: 8163 / CC1/2: 0.354 / Rrim(I) all: 1.37

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 2.26→48.63 Å / SU ML: 0.3126 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 24.4892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 2387 5.04 %
Rwork0.1926 44945 -
obs0.1933 47332 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.77 Å2
Refinement stepCycle: LAST / Resolution: 2.26→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 23 57 3407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01653429
X-RAY DIFFRACTIONf_angle_d2.02824647
X-RAY DIFFRACTIONf_chiral_restr0.0952513
X-RAY DIFFRACTIONf_plane_restr0.0101597
X-RAY DIFFRACTIONf_dihedral_angle_d15.62621280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.310.35821370.34632605X-RAY DIFFRACTION97.65
2.31-2.360.35951360.32872635X-RAY DIFFRACTION100
2.36-2.420.29671400.30992640X-RAY DIFFRACTION99.96
2.42-2.480.31400.3132655X-RAY DIFFRACTION100
2.48-2.540.31751420.31432650X-RAY DIFFRACTION99.96
2.54-2.620.27871420.30082615X-RAY DIFFRACTION99.96
2.62-2.70.26571400.2722663X-RAY DIFFRACTION100
2.7-2.80.27531400.25962680X-RAY DIFFRACTION100
2.8-2.910.28561410.24512626X-RAY DIFFRACTION100
2.91-3.040.30181440.25982656X-RAY DIFFRACTION100
3.04-3.20.1851380.20732612X-RAY DIFFRACTION99.96
3.2-3.410.25221380.18192665X-RAY DIFFRACTION100
3.41-3.670.18571440.17242629X-RAY DIFFRACTION100
3.67-4.040.15641450.14932656X-RAY DIFFRACTION100
4.04-4.620.15241340.14322658X-RAY DIFFRACTION100
4.62-5.820.14421480.14312657X-RAY DIFFRACTION100
5.82-48.630.17571380.15392643X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.5949052554 Å / Origin y: 0.940571520959 Å / Origin z: -13.9323866527 Å
111213212223313233
T0.273482616927 Å2-0.00956505589189 Å2-0.0294871296104 Å2-0.279235895522 Å2-0.00401680223032 Å2--0.238330046265 Å2
L1.57397819565 °20.0215838501284 °2-0.28450192905 °2-1.26292164078 °20.241767936197 °2--0.764177909209 °2
S0.0297036919358 Å °-0.182920564163 Å °0.0389534485345 Å °0.0937812536893 Å °-0.0625797247851 Å °0.0259773998645 Å °0.0250306083237 Å °0.0711898529201 Å °2.04898135038E-10 Å °
Refinement TLS groupSelection details: (chain A and resseq 19:444)

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