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- PDB-2jd5: Sky1p bound to Npl3p-derived substrate peptide -

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Basic information

Entry
Database: PDB / ID: 2jd5
TitleSky1p bound to Npl3p-derived substrate peptide
Components
  • NUCLEOLAR PROTEIN 3Nucleolus
  • SERINE/THREONINE-PROTEIN KINASE SKY1
KeywordsTRANSFERASE / MRNA EXPORT PROTEIN / SERINE/THREONINE-PROTEIN KINASE / KINASE / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / eukaryotic initiation factor 4G binding / intracellular monoatomic cation homeostasis / intracellular monoatomic ion homeostasis / regulation of mRNA processing / mRNA splice site recognition / poly(A) binding / stress granule disassembly / regulation of cell size / spliceosomal complex assembly ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / eukaryotic initiation factor 4G binding / intracellular monoatomic cation homeostasis / intracellular monoatomic ion homeostasis / regulation of mRNA processing / mRNA splice site recognition / poly(A) binding / stress granule disassembly / regulation of cell size / spliceosomal complex assembly / RNA polymerase II complex binding / translational termination / positive regulation of transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / cytoplasmic stress granule / positive regulation of protein import into nucleus / ribosome biogenesis / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / ribonucleoprotein complex / phosphorylation / protein serine kinase activity / mRNA binding / protein serine/threonine kinase activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Npl3, RNA recognition motif 1 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Npl3, RNA recognition motif 1 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/arginine (SR)-type shuttling mRNA binding protein NPL3 / Serine/threonine-protein kinase SKY1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNolen, B. / Lukasiewicz, R. / Adams, J.A. / Huang, D. / Ghosh, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Rgg Domain of Npl3P Recruits Sky1P Through Docking Interactions
Authors: Lukasiewicz, R. / Nolen, B. / Adams, J.A. / Ghosh, G.
History
DepositionJan 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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: SERINE/THREONINE-PROTEIN KINASE SKY1
B: SERINE/THREONINE-PROTEIN KINASE SKY1
C: NUCLEOLAR PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1637
Polymers86,9223
Non-polymers2414
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.328, 88.558, 134.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE SKY1 / SKY1P / SRPK


Mass: 43009.066 Da / Num. of mol.: 2 / Fragment: RESIDUES 138-306,539-742
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q03656, non-specific serine/threonine protein kinase
#2: Protein/peptide NUCLEOLAR PROTEIN 3 / Nucleolus / MITOCHONDRIAL TARGETING SUPPRESSOR 1 PROTEIN / NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 1 / NPL3P


Mass: 904.007 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 408-414 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q01560
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT LACKS THE N-TERMINUS (1-137) AS WELL AS THE SPACER DOMAIN (305-540) PEPTIDE C ...THIS CONSTRUCT LACKS THE N-TERMINUS (1-137) AS WELL AS THE SPACER DOMAIN (305-540) PEPTIDE C CONTAINS THE LAST 7 AMINO ACIDS OF NPL3P

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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: 2.5 Å3/Da / Density % sol: 49 %
Crystal growpH: 7
Details: 1.5M AMMONIUM SULFATE, 10% ETHYLENE GLYCOL, 10 MM SODIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 30449 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HOW

1how


Resolution: 2.5→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 344404.56 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1224 4.9 %RANDOM
Rwork0.21 ---
obs0.21 25101 82.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.7 Å2 / ksol: 0.349259 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20 Å20 Å2
2---5.28 Å20 Å2
3---1.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 12 133 5920
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it3.052
X-RAY DIFFRACTIONc_scangle_it3.982.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 146 4.8 %
Rwork0.243 2909 -
obs--61.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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