[English] 日本語
Yorodumi
- PDB-9uju: The structure of Egalitarian in complex with the K10 mRNA localiz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9uju
TitleThe structure of Egalitarian in complex with the K10 mRNA localization signal reveals a modular binding surface required for function
Components
  • ALA-LEU-GLU-PHE-ALA
  • Egalitarian, isoform B
  • RNA (46-MER)
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 / mRNA transport / 3'-5' exonuclease activity / mRNA binding / metal ion binding
Similarity search - Function
: / Egalitarian winged helix domain / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Egalitarian, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: RNA (46-MER)
D: RNA (46-MER)
C: Egalitarian, isoform B
A: Egalitarian, isoform B
X: ALA-LEU-GLU-PHE-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,84213
Polymers101,5215
Non-polymers3218
Water30617
1
B: RNA (46-MER)
A: Egalitarian, isoform B
X: ALA-LEU-GLU-PHE-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1165
Polymers51,0353
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RNA (46-MER)
C: Egalitarian, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7268
Polymers50,4862
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.504, 106.799, 139.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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

-
Components

#1: RNA chain RNA (46-MER)


Mass: 15231.974 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
#2: Protein Egalitarian, isoform B / Egalitarian / isoform C


Mass: 35253.820 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: Escherichia coli (E. coli) / References: UniProt: Q9W1K4
#3: Protein/peptide ALA-LEU-GLU-PHE-ALA


Mass: 549.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 50 mM sodium citrate, pH 4.8, 30% (w/v) MPD, 10 mM CaCl2, 2.5 mM Spermine

-
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: Apr 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 36673 / % possible obs: 99.8 % / Redundancy: 7.02 % / CC1/2: 0.999 / Net I/σ(I): 0.17
Reflection shellResolution: 3.08→3.27 Å / Num. unique obs: 5931 / CC1/2: 0.702 / Rrim(I) all: 1.41

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ITasser

Resolution: 3.08→44.48 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2916 982 5.01 %
Rwork0.2402 --
obs0.2425 19620 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 1954 8 17 5828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146082
X-RAY DIFFRACTIONf_angle_d2.0268714
X-RAY DIFFRACTIONf_dihedral_angle_d16.9812404
X-RAY DIFFRACTIONf_chiral_restr0.111124
X-RAY DIFFRACTIONf_plane_restr0.009787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.240.3591370.32712600X-RAY DIFFRACTION99
3.24-3.440.3751380.28532617X-RAY DIFFRACTION100
3.44-3.710.33091380.25412623X-RAY DIFFRACTION100
3.71-4.080.27891390.22952644X-RAY DIFFRACTION100
4.08-4.670.28621400.21762652X-RAY DIFFRACTION100
4.67-5.880.28411410.24222692X-RAY DIFFRACTION100
5.89-44.480.26821490.22772810X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.688 Å / Origin y: -4.6914 Å / Origin z: -30.664 Å
111213212223313233
T0.44 Å20.0656 Å2-0.0271 Å2-0.4855 Å20.1349 Å2--0.5316 Å2
L-0.4259 °21.1027 °2-0.0999 °2--0.1038 °2-0.8706 °2--0.639 °2
S-0.2409 Å °0.1434 Å °-0.0141 Å °0.0166 Å °0.4003 Å °0.7347 Å °-0.0436 Å °-0.4704 Å °-0 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more