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- PDB-3beg: Crystal structure of SR protein kinase 1 complexed to its substra... -

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Basic information

Entry
Database: PDB / ID: 3beg
TitleCrystal structure of SR protein kinase 1 complexed to its substrate ASF/SF2
Components
  • Serine/threonine-protein kinase SRPK1
  • Splicing factor, arginine/serine-rich 1
KeywordsTransferase/Splicing / kinase / sr protein kinase / sr protein / pre-mRNA splicing / ATP-binding / Chromosome partition / Differentiation / mRNA processing / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / Transferase / Methylation / RNA-binding / Spliceosome / Transferase-Splicing COMPLEX
Function / homology
Function and homology information


DNA topoisomerase binding / protein kinase B binding / sperm DNA condensation / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of mRNA processing / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination ...DNA topoisomerase binding / protein kinase B binding / sperm DNA condensation / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of mRNA processing / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / regulation of RNA splicing / oligodendrocyte differentiation / mRNA 5'-splice site recognition / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / positive regulation of viral genome replication / Replacement of protamines by nucleosomes in the male pronucleus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of RNA splicing / liver regeneration / chromosome segregation / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / nuclear envelope / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / chromatin / magnesium ion binding / endoplasmic reticulum / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / SRSF1, RNA recognition motif 1 / : / : / 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 ...: / SRSF1, RNA recognition motif 1 / : / : / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ALANINE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHOSERINE / Serine/arginine-rich splicing factor 1 / SRSF protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsNgo, J.C. / Giang, K. / Chakrabarti, S. / Ma, C.-T. / Huynh, N. / Hagopian, J. / Dorrestein, P.C. / Fu, X.-D. / Adams, J.A. / Ghosh, G.
CitationJournal: Mol.Cell / Year: 2008
Title: A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by SRPK1
Authors: Ngo, J.C. / Giang, K. / Chakrabarti, S. / Ma, C.-T. / Huynh, N. / Hagopian, J. / Dorrestein, P.C. / Fu, X.-D. / Adams, J.A. / Ghosh, G.
History
DepositionNov 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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 SRPK1
B: Splicing factor, arginine/serine-rich 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1845
Polymers56,4032
Non-polymers7803
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.406, 117.525, 193.554
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Serine/threonine-protein kinase SRPK1 / Serine/arginine-rich protein-specific kinase 1 / SR-protein-specific kinase 1 / SFRS protein kinase 1


Mass: 43381.836 Da / Num. of mol.: 1
Fragment: Kinase domain of SRPK1; UNP residues 229-426, 645-826
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96SB4, non-specific serine/threonine protein kinase
#2: Protein Splicing factor, arginine/serine-rich 1 / pre-mRNA-splicing factor SF2 / P33 subunit / Alternative-splicing factor 1 / ASF-1


Mass: 13021.483 Da / Num. of mol.: 1 / Fragment: UNP residues 105-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFRS1, ASF, SF2, SF2P33 / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07955
#3: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P
#4: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Nonpolymer detailsDIPEPTIDE WITH SEQUENCE SEP-ALA

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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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate, 0.2M sodium acetate, 5% ethanol, 15% PEGMME 5000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 13862 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rsym value: 0.058 / Net I/σ(I): 19.9
Reflection shellResolution: 2.9→2.976 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.54 / Rsym value: 0.443 / % possible all: 62.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→38.4 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 45.222 / SU ML: 0.351 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.298 707 5.1 %RANDOM
Rwork0.237 ---
obs0.24 13153 92.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.17 Å2
Baniso -1Baniso -2Baniso -3
1--6.41 Å20 Å20 Å2
2---3.21 Å20 Å2
3---9.62 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 46 0 3446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223524
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9644790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8875431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61823.846156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.16515.026579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4931520
X-RAY DIFFRACTIONr_chiral_restr0.1050.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022634
X-RAY DIFFRACTIONr_nbd_refined0.2320.21701
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.22
X-RAY DIFFRACTIONr_mcbond_it0.4051.52209
X-RAY DIFFRACTIONr_mcangle_it0.75223465
X-RAY DIFFRACTIONr_scbond_it0.99831505
X-RAY DIFFRACTIONr_scangle_it1.6964.51325
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 39 -
Rwork0.415 590 -
all-629 -
obs--58.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9965-0.11990.29154.7521-2.25123.93760.1496-0.13880.41920.6916-0.5407-0.6615-0.19280.23480.3911-0.5405-0.2138-0.1509-0.27920.09920.151318.69919.35267.049
23.05083.5088-3.20727.8326-4.93443.90880.29120.13560.45010.1370.21661.0542-0.2179-0.2049-0.5077-0.5933-0.0067-0.0655-0.1136-0.04130.3906-5.60314.00663.514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA69 - 23512 - 178
2X-RAY DIFFRACTION1AA475 - 655201 - 381
3X-RAY DIFFRACTION2BB121 - 19617 - 92
4X-RAY DIFFRACTION2BB201 - 21097 - 106

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