[English] 日本語
Yorodumi
- PDB-4qqb: Structural basis for the assembly of the SXL-UNR translation regu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qqb
TitleStructural basis for the assembly of the SXL-UNR translation regulatory complex
Components
  • Protein sex-lethal
  • Upstream of N-ras, isoform A
  • msl2 mRNA
KeywordsTRANLATION/RNA / RNA binding domains / RNA recognition motif / RRM / cold shock domain / CSD / RNA binding / translation regulation / dosage compensation / TRANSCRIPTION-RNA complex / TRANLATION-RNA complex
Function / homology
Function and homology information


sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / sex-chromosome dosage compensation / regulation of stem cell division ...sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / sex-chromosome dosage compensation / regulation of stem cell division / sex determination / poly-pyrimidine tract binding / messenger ribonucleoprotein complex / sex differentiation / alternative mRNA splicing, via spliceosome / negative regulation of receptor signaling pathway via JAK-STAT / pre-mRNA binding / poly(A) binding / positive regulation of smoothened signaling pathway / reciprocal meiotic recombination / regulation of mRNA splicing, via spliceosome / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / oogenesis / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / mRNA 3'-UTR binding / mRNA 5'-UTR binding / negative regulation of translation / nucleic acid binding / protein stabilization / molecular adaptor activity / ribonucleoprotein complex / protein-containing complex / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sex-lethal splicing factor / Paraneoplastic encephalomyelitis antigen / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / RRM (RNA recognition motif) domain ...Sex-lethal splicing factor / Paraneoplastic encephalomyelitis antigen / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / RRM (RNA recognition motif) domain / Nucleic acid-binding proteins / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein sex-lethal / Upstream of N-ras, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHennig, J. / Popowicz, G.M. / Sattler, M.
CitationJournal: Nature / Year: 2014
Title: Structural basis for the assembly of the Sxl-Unr translation regulatory complex.
Authors: Hennig, J. / Militti, C. / Popowicz, G.M. / Wang, I. / Sonntag, M. / Geerlof, A. / Gabel, F. / Gebauer, F. / Sattler, M.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: msl2 mRNA
A: Protein sex-lethal
C: msl2 mRNA
B: Protein sex-lethal
X: Upstream of N-ras, isoform A
Y: Upstream of N-ras, isoform A


Theoretical massNumber of molelcules
Total (without water)67,4316
Polymers67,4316
Non-polymers00
Water0
1
P: msl2 mRNA
A: Protein sex-lethal
X: Upstream of N-ras, isoform A


Theoretical massNumber of molelcules
Total (without water)33,7153
Polymers33,7153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: msl2 mRNA
B: Protein sex-lethal
Y: Upstream of N-ras, isoform A


Theoretical massNumber of molelcules
Total (without water)33,7153
Polymers33,7153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.360, 110.970, 139.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.983199, 0.094104, -0.156409), (0.084605, 0.994204, 0.06633), (0.161744, 0.051983, -0.985463)-48.08398, -4.05555, -1.8677
Detailsmonomeric complex of three different entities (heterotrimer)

-
Components

#1: RNA chain msl2 mRNA


Mass: 5712.380 Da / Num. of mol.: 2 / Fragment: site F 18-mer / Source method: obtained synthetically / Details: synthetic RNA (purchased from IBA)
#2: Protein Protein sex-lethal


Mass: 19797.510 Da / Num. of mol.: 2 / Fragment: RRM1-RRM2, UNP residues 122-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sxl, Sx1, CG43770 / Production host: Escherichia coli (E. coli) / References: UniProt: P19339
#3: Protein Upstream of N-ras, isoform A


Mass: 8205.391 Da / Num. of mol.: 2 / Fragment: CSD1, UNP residues 185-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Unr, CG7015, Dmel_CG7015 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VSK3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.4 Å3/Da / Density % sol: 77.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M LiSO4, PEG3350 1-5 %, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 36389 / Num. obs: 36315 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.85 Å / % possible all: 99.4

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B7F

1b7f


Resolution: 2.8→19.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.59 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.53 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23564 1320 5.1 %RANDOM
Rwork0.19817 ---
obs0.20011 24714 71 %-
all-34809 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å2-0 Å2
2---1.07 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 716 0 0 4556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0184702
X-RAY DIFFRACTIONr_bond_other_d0.0020.024098
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.8366496
X-RAY DIFFRACTIONr_angle_other_deg0.8439448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7795478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13523.125192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43415700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5291540
X-RAY DIFFRACTIONr_chiral_restr0.0740.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021100
X-RAY DIFFRACTIONr_mcbond_it4.0219.9581924
X-RAY DIFFRACTIONr_mcbond_other4.0219.9571923
X-RAY DIFFRACTIONr_mcangle_it6.78114.9122398
X-RAY DIFFRACTIONr_mcangle_other6.77914.9142399
X-RAY DIFFRACTIONr_scbond_it3.75310.0742778
X-RAY DIFFRACTIONr_scbond_other3.75310.0742779
X-RAY DIFFRACTIONr_scangle_other6.37214.954099
X-RAY DIFFRACTIONr_long_range_B_refined10.22881.6115320
X-RAY DIFFRACTIONr_long_range_B_other10.22781.6185321
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 45 -
Rwork0.477 787 -
obs--31.85 %

+
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