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- PDB-2x1g: Crystal structure of Importin13 - Mago-Y14 complex -

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Basic information

Entry
Database: PDB / ID: 2x1g
TitleCrystal structure of Importin13 - Mago-Y14 complex
Components
  • CADMUS
  • PROTEIN MAGO NASHI
  • RNA-BINDING PROTEIN 8A
KeywordsTRANSPORT PROTEIN / DEVELOPMENTAL PROTEIN / MRNA PROCESSING / NUCLEAR TRANSPORT / MRNA SPLICING / MRNA TRANSPORT
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 / phototaxis / neuron-neuron synaptic transmission / exon-exon junction complex / import into nucleus / NLS-dependent protein nuclear import complex / nuclear export / positive regulation of protein-containing complex disassembly / oogenesis / precatalytic spliceosome / mRNA transport / catalytic step 2 spliceosome / RNA splicing / modulation of chemical synaptic transmission / protein localization / small GTPase binding / mRNA splicing, via spliceosome / microtubule cytoskeleton organization / protein import into nucleus / mRNA binding / synapse / positive regulation of gene expression / RNA binding / nucleus / cytoplasm
Similarity search - Function
Importin 13 repeat / Importin 13, repeat 1 / Importin 13 repeat / Importin 13 repeat / Mago nashi protein / Mago nashi / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily ...Importin 13 repeat / Importin 13, repeat 1 / Importin 13 repeat / Importin 13 repeat / Mago nashi protein / Mago nashi / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein mago nashi / RNA-binding protein 8A / Importin-13
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsBono, F. / Cook, A.G. / Gruenwald, M. / Ebert, J. / Conti, E.
CitationJournal: Mol.Cell / Year: 2010
Title: Nuclear Import Mechanism of the Ejc Component Mago- Y14 Revealed by Structural Studies of Importin 13.
Authors: Bono, F. / Cook, A.G. / Grunwald, M. / Ebert, J. / Conti, E.
History
DepositionDec 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Data collection / Refinement description ...Data collection / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details ..._exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 20, 2023Group: 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: RNA-BINDING PROTEIN 8A
B: PROTEIN MAGO NASHI
C: RNA-BINDING PROTEIN 8A
D: PROTEIN MAGO NASHI
F: CADMUS
G: CADMUS


Theoretical massNumber of molelcules
Total (without water)295,6286
Polymers295,6286
Non-polymers00
Water00
1
A: RNA-BINDING PROTEIN 8A
B: PROTEIN MAGO NASHI
F: CADMUS


Theoretical massNumber of molelcules
Total (without water)147,8143
Polymers147,8143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-20.9 kcal/mol
Surface area60130 Å2
MethodPISA
2
C: RNA-BINDING PROTEIN 8A
D: PROTEIN MAGO NASHI
G: CADMUS


Theoretical massNumber of molelcules
Total (without water)147,8143
Polymers147,8143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-20.9 kcal/mol
Surface area60110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.569, 100.792, 93.923
Angle α, β, γ (deg.)89.83, 110.18, 90.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99997, -0.00797, -0.00154), (-0.00797, 0.99997, -0.00181), (0.00154, -0.00181, -1)
Vector: 20.88311, -50.2963, -19.15612)

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Components

#1: Protein RNA-BINDING PROTEIN 8A / PROTEIN TSUNAGI / Y14


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 GOLD PLYSS / References: UniProt: Q9V535
#2: Protein PROTEIN MAGO NASHI


Mass: 17335.797 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 GOLD PLYSS / References: UniProt: P49028
#3: Protein CADMUS / IMPORTIN13 / LD35896P


Mass: 111436.164 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 GOLD PLYSS / References: UniProt: Q9VEC5

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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: 2.48 Å3/Da / Density % sol: 50.43 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978, 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.9791
ReflectionResolution: 3.35→50 Å / Num. obs: 39374 / % possible obs: 96.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2 % / Biso Wilson estimate: 82.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.7
Reflection shellResolution: 3.35→3.53 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.5 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HL6

1hl6


Resolution: 3.35→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1972 4.8 %RANDOM
Rwork0.267 ---
obs0.267 39362 96.3 %-
Solvent computationBsol: 106.33 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 97.3 Å2
Baniso -1Baniso -2Baniso -3
1--12.133 Å2-1.995 Å2-0.354 Å2
2--3.18 Å20.123 Å2
3---8.954 Å2
Refinement stepCycle: LAST / Resolution: 3.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16076 0 0 0 16076
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.25
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
Refine LS restraints NCSNCS model details: CONSTRAINTS
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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