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- PDB-1oo0: Crystal structure of the Drosophila Mago nashi-Y14 complex -

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Basic information

Entry
Database: PDB / ID: 1oo0
TitleCrystal structure of the Drosophila Mago nashi-Y14 complex
Components
  • CG8781-PA
  • Mago nashi protein
KeywordsSIGNALING PROTEIN / RNA recognition motif / splicing / Protein complex / Exon junction complex
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 / protein localization / microtubule cytoskeleton organization / mRNA splicing, via spliceosome / 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
BETA-MERCAPTOETHANOL / STRONTIUM ION / Protein mago nashi / RNA-binding protein 8A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsShi, H. / Xu, R.M.
CitationJournal: Genes Dev. / Year: 2003
Title: Crystal structure of the Drosophila Mago nashi-Y14 complex
Authors: Shi, H. / Xu, R.M.
History
DepositionMar 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mago nashi protein
B: CG8781-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6989
Polymers30,0342
Non-polymers6647
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-76 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.027, 52.387, 52.862
Angle α, β, γ (deg.)90.00, 104.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Mago nashi protein


Mass: 17335.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: MAGO / Plasmid: pMR101 (His-Mago) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P49028
#2: Protein CG8781-PA / drosophila Y14


Mass: 12698.081 Da / Num. of mol.: 1 / Fragment: Middle Fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: TSU / Plasmid: pGEX-KG (Y14) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9V535

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Non-polymers , 5 types, 145 molecules

#3: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.38 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: MPD, sodium acetate, Strontium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125-30 mg/mlprotein1drop
210 mMHEPES1droppH8.0
35 %glycerol1drop
4500 mM1dropNaCl
5100 mMsodium acetate1reservoirpH5.8
630 %MPD1reservoir
710 mM1reservoirSrCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 22, 2002 / Details: mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Silicon (111) chanel cutMADMx-ray1
2Silicon (111) chanel cutSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 23235 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.85 Å / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 23222 / Num. measured all: 155205 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 81.4 % / Rmerge(I) obs: 0.346

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.85→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 2239 random
Rwork0.215 --
obs0.215 22618 -
all-23235 -
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 37 138 2111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.77
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 1.85→1.86 Å /
RfactorNum. reflection
Rfree0.36 25
Rwork0.29 -
obs-319
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.261
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08

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