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- PDB-6s8r: D. melanogaster RNA helicase Me31B in complex with GIGYF -

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Basic information

Entry
Database: PDB / ID: 6s8r
TitleD. melanogaster RNA helicase Me31B in complex with GIGYF
Components
  • ATP-dependent RNA helicase me31b
  • GIGYF family protein CG11148
KeywordsRNA BINDING PROTEIN / Translation / Translational control / mRNA decay / miRNA
Function / homology
Function and homology information


positive regulation of post-transcriptional gene silencing / sensory dendrite / translation repressor complex / : / regulation of olfactory learning / mRNA decay by 5' to 3' exoribonuclease / regulation of neuron projection arborization / follicle cell of egg chamber development / : / pole cell formation ...positive regulation of post-transcriptional gene silencing / sensory dendrite / translation repressor complex / : / regulation of olfactory learning / mRNA decay by 5' to 3' exoribonuclease / regulation of neuron projection arborization / follicle cell of egg chamber development / : / pole cell formation / neuronal ribonucleoprotein granule / messenger ribonucleoprotein complex / eukaryotic translation initiation factor 4F complex / deadenylation-dependent decapping of nuclear-transcribed mRNA / miRNA-mediated post-transcriptional gene silencing / habituation / regulation of defense response to virus / P-body assembly / P granule / muscle cell cellular homeostasis / negative regulation of cytoplasmic translation / stress granule assembly / translation repressor activity / mRNA regulatory element binding translation repressor activity / regulation of autophagy / P-body / cytoplasmic ribonucleoprotein granule / neuron cellular homeostasis / cytoplasmic stress granule / postsynapse / RNA helicase activity / RNA helicase / hydrolase activity / mRNA binding / neuronal cell body / endoplasmic reticulum / RNA binding / ATP binding / cytoplasm
Similarity search - Function
GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / 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 ...GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / 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 / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ATP-dependent RNA helicase me31b / GIGYF family protein Gyf
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsPeter, D. / Valkov, E.
CitationJournal: Genes Dev. / Year: 2019
Title: Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression.
Authors: Peter, D. / Ruscica, V. / Bawankar, P. / Weber, R. / Helms, S. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase me31b
B: GIGYF family protein CG11148
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0886
Polymers22,8522
Non-polymers2364
Water63135
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-15 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.440, 41.960, 122.670
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 ATP-dependent RNA helicase me31b / Maternal expression at 31B


Mass: 20004.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: me31B, CG4916 / Production host: Escherichia coli (E. coli) / References: UniProt: P23128, RNA helicase
#2: Protein/peptide GIGYF family protein CG11148


Mass: 2847.999 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG11148 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KQM6
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate (pH 5.0), 0.15 M ammonium chloride, 16% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9996 Å / Relative weight: 1
ReflectionResolution: 2.4→42 Å / Num. obs: 7712 / % possible obs: 95.8 % / Redundancy: 10.4 % / Biso Wilson estimate: 27.21 Å2 / Rsym value: 0.188 / Net I/σ(I): 8.91
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 9.7 % / Num. unique obs: 522 / Rsym value: 1.06 / % possible all: 88.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ANR

5anr


Resolution: 2.41→39.7 Å / SU ML: 0.2761 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.1878
RfactorNum. reflection% reflection
Rfree0.2612 326 4.79 %
Rwork0.2028 --
obs0.2056 6800 85.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.19 Å2
Refinement stepCycle: LAST / Resolution: 2.41→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 16 35 1621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331616
X-RAY DIFFRACTIONf_angle_d0.45922178
X-RAY DIFFRACTIONf_chiral_restr0.0407237
X-RAY DIFFRACTIONf_plane_restr0.0023285
X-RAY DIFFRACTIONf_dihedral_angle_d6.6858954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-3.040.31971360.23022633X-RAY DIFFRACTION71.33
3.04-39.70.23891900.19343841X-RAY DIFFRACTION99.07

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