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- PDB-5nt7: Structure of the LOTUS domain of Oskar in complex with the C-term... -

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Basic information

Entry
Database: PDB / ID: 5nt7
TitleStructure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa
Components
  • ATP-dependent RNA helicase vasa, isoform A
  • Maternal effect protein oskar
Keywordshydrolase/hydrolase regulator / DEAD-box RNA helicase / ATPase / RNA binding / regulator / stimulator / germ plasm / nuage / LOTUS / hydrolase- hydrolase regulator complex / hydrolase-hydrolase regulator complex
Function / homology
Function and homology information


posterior abdomen determination / pole plasm mRNA localization / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte microtubule cytoskeleton polarization / pole plasm / posterior cell cortex / thermosensory behavior / P granule organization ...posterior abdomen determination / pole plasm mRNA localization / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte microtubule cytoskeleton polarization / pole plasm / posterior cell cortex / thermosensory behavior / P granule organization / pole plasm assembly / pole cell formation / segmentation / secondary piRNA processing / visual behavior / gamete generation / P granule / germ cell nucleus / cortical actin cytoskeleton organization / oogenesis / germ cell development / protein localization to nucleus / long-term memory / regulation of mRNA stability / visual learning / intracellular protein localization / cell cortex / cell differentiation / RNA helicase activity / endosome / RNA helicase / mRNA binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
OSK domain / Ded1/Dbp1, DEAD-box helicase domain / OSK domain / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / SGNH hydrolase superfamily / DEAD-box subfamily ATP-dependent helicases signature. ...OSK domain / Ded1/Dbp1, DEAD-box helicase domain / OSK domain / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / SGNH hydrolase superfamily / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / Nucleotidyltransferase; domain 5 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase vasa / Maternal effect protein oskar
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJeske, M. / Ephrussi, A. / Mueller, C.W.
CitationJournal: Genes Dev. / Year: 2017
Title: The LOTUS domain is a conserved DEAD-box RNA helicase regulator essential for the recruitment of Vasa to the germ plasm and nuage.
Authors: Jeske, M. / Muller, C.W. / Ephrussi, A.
History
DepositionApr 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ATP-dependent RNA helicase vasa, isoform A
A: Maternal effect protein oskar
C: Maternal effect protein oskar
D: ATP-dependent RNA helicase vasa, isoform A


Theoretical massNumber of molelcules
Total (without water)60,3304
Polymers60,3304
Non-polymers00
Water11,043613
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-17 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.950, 39.040, 97.480
Angle α, β, γ (deg.)89.28, 91.85, 99.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ATP-dependent RNA helicase vasa, isoform A / Antigen Mab46F11


Mass: 18247.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal residues GH (Glycine, Histidine) stem from the TEV cleavage site
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: vas, vasa, CG46283 / Production host: Escherichia coli (E. coli) / References: UniProt: P09052, RNA helicase
#2: Protein Maternal effect protein oskar


Mass: 11917.491 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal residues GPLGS stem from the 3C cleavage site
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: osk, CG10901 / Production host: Escherichia coli (E. coli) / References: UniProt: P25158
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 7.5, 200 mM potassium thiocyanate, 16% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97908 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 102457 / % possible obs: 91.4 % / Redundancy: 2.16 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.44
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.18 % / Rmerge(I) obs: 1.382 / Mean I/σ(I) obs: 0.74 / CC1/2: 0.394 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A49, 2DB3

5a49

2db3


Resolution: 1.4→48.713 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.95
RfactorNum. reflection% reflection
Rfree0.1991 1996 1.95 %
Rwork0.169 --
obs0.1696 102415 91.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→48.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 0 613 4450

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