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- PDB-1rk8: Structure of the cytosolic protein PYM bound to the Mago-Y14 core... -

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Basic information

Entry
Database: PDB / ID: 1rk8
TitleStructure of the cytosolic protein PYM bound to the Mago-Y14 core of the exon junction complex
Components
  • CG8781-PA protein
  • Mago nashi protein
  • Within the bgcn gene intron protein
KeywordsTRANSLATION / mRNA processing / RRM / RBD / NMD / oskar mRNA localization
Function / homology
Function and homology information


exon-exon junction complex disassembly / 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) / exon-exon junction complex binding / oocyte microtubule cytoskeleton polarization ...exon-exon junction complex disassembly / 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) / exon-exon junction complex binding / oocyte microtubule cytoskeleton polarization / mRNA Splicing - Major Pathway / 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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / precatalytic spliceosome / oogenesis / mRNA transport / catalytic step 2 spliceosome / RNA splicing / mRNA splicing, via spliceosome / microtubule cytoskeleton organization / intracellular protein localization / mRNA binding / positive regulation of gene expression / RNA binding / nucleus / cytoplasm
Similarity search - Function
WIBG, N-terminal domain superfamily / Partner of Y14 and mago / Mago binding / Mago binding / WIBG, Mago-binding / Mago nashi protein / Mago nashi / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif ...WIBG, N-terminal domain superfamily / Partner of Y14 and mago / Mago binding / Mago binding / WIBG, Mago-binding / 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 / Partner of Y14 and mago / RNA-binding protein 8A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBono, F. / Ebert, J. / Guettler, T. / Izaurralde, E. / Conti, E.
CitationJournal: EMBO Rep. / Year: 2004
Title: Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex
Authors: Bono, F. / Ebert, J. / Unterholzner, L. / Guettler, T. / Izaurralde, E. / Conti, E.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 28, 2021Group: Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine.ls_percent_reflns_obs / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: CG8781-PA protein
B: Mago nashi protein
C: Within the bgcn gene intron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1086
Polymers42,9873
Non-polymers1203
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.357, 106.357, 58.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein CG8781-PA protein / CG8781-PA


Mass: 19042.127 Da / Num. of mol.: 1 / Fragment: RBD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: tsu / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V535
#2: Protein Mago nashi protein / CG9401-PA


Mass: 17335.797 Da / Num. of mol.: 1 / Fragment: full-length
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: MAGO,MGN,CG9401 / Production host: Escherichia coli (E. coli) / References: UniProt: P49028
#3: Protein Within the bgcn gene intron protein / PYM protein / CG30176-PA


Mass: 6609.504 Da / Num. of mol.: 1 / Fragment: N-terminal domain (residues 1-58)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: WIBG,PYM,CG30176/CG10330 / Production host: Escherichia coli (E. coli) / References: UniProt: P82804
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.83 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7.5
Details: HEPES, PEG 400, CaCl2, pH 7.5, VAPOR DIFFUSION, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0091 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0091 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 26797 / Num. obs: 26797 / % possible obs: 99.8 %
Reflection shellResolution: 1.9→2 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1047 -random
Rwork0.235 ---
all0.235 26797 --
obs0.235 25750 96.1 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 3 142 2073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg1.19

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