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- PDB-1hl6: A novel mode of RBD-protein recognition in the Y14-mago complex -

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Basic information

Entry
Database: PDB / ID: 1hl6
TitleA novel mode of RBD-protein recognition in the Y14-mago complex
Components
  • CG8781 PROTEIN
  • MAGO NASHI PROTEIN
KeywordsSIGNAL PROTEIN / RDB / EXON-EXON JUNCTION / OSKAR / RNP / NMD
Function / homology
Function and homology information


establishment of pole plasm mRNA localization / oocyte nucleus localization involved in oocyte dorsal/ventral axis specification / maintenance of pole plasm mRNA location / Transport of Mature mRNA derived from an Intron-Containing Transcript / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA Splicing - Major Pathway / oocyte microtubule cytoskeleton polarization / oocyte anterior/posterior axis specification ...establishment of pole plasm mRNA localization / oocyte nucleus localization involved in oocyte dorsal/ventral axis specification / maintenance of pole plasm mRNA location / Transport of Mature mRNA derived from an Intron-Containing Transcript / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA Splicing - Major Pathway / oocyte microtubule cytoskeleton polarization / oocyte anterior/posterior axis specification / oocyte microtubule cytoskeleton organization / pole plasm / germarium-derived oocyte fate determination / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification / pole plasm assembly / exon-exon junction complex / import into nucleus / NLS-dependent protein nuclear import complex / precatalytic spliceosome / oogenesis / mRNA transport / catalytic step 2 spliceosome / RNA splicing / mRNA splicing, via spliceosome / microtubule cytoskeleton organization / protein localization / mRNA binding / positive regulation of gene expression / RNA binding / nucleus / cytoplasm
Similarity search - Function
Mago nashi protein / Mago nashi / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...Mago nashi protein / Mago nashi / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein mago nashi / RNA-binding protein 8A
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsFribourg, S. / Gatfield, D. / Yao, W. / Izaurralde, E. / Conti, E.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: A Novel Mode of Rbd-Protein Recognition in the Y14-Mago Complex
Authors: Fribourg, S. / Gatfield, D. / Izaurralde, E. / Conti, E.
History
DepositionMar 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG8781 PROTEIN
B: MAGO NASHI PROTEIN
C: CG8781 PROTEIN
D: MAGO NASHI PROTEIN


Theoretical massNumber of molelcules
Total (without water)73,2644
Polymers73,2644
Non-polymers00
Water1,802100
1
A: CG8781 PROTEIN
B: MAGO NASHI PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,6322
Polymers36,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CG8781 PROTEIN
D: MAGO NASHI PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,6322
Polymers36,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)140.177, 140.177, 68.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.02464, 0.98232, -0.18559), (0.56709, -0.13915, -0.81182), (-0.82329, -0.12525, -0.55364)
Vector: -7.97887, 78.60268, 89.443)

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Components

#1: Protein CG8781 PROTEIN


Mass: 19042.127 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) / Strain (production host): BL21(DE3) / References: UniProt: Q9V535
#2: Protein MAGO NASHI PROTEIN / MAGO


Mass: 17590.105 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) / Strain (production host): BL21(DE3) / References: UniProt: P49028
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.3 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.5 / Details: SODIUM CITRATE PH5.25 PEG 3000 12-20%, pH 5.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(w/v)PEG30001reservoir
20.1 Msodium citrate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 23227 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
Lowest resolution: 2.64 Å / % possible obs: 99.4 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 -5 %RANDOM
Rwork0.224 ---
obs0.224 104735 100 %-
Displacement parametersBiso mean: 31.3477 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 0 100 4285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007047
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.31549
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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