[English] 日本語
Yorodumi
- PDB-1wbp: SRPK1 bound to 9mer docking motif peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wbp
TitleSRPK1 bound to 9mer docking motif peptide
Components
  • MEMBRANE-ASSOCIATED GUANYLATE KINASE, WW AND PDZ DOMAIN-CONTAINING PROTEIN 1
  • SERINE/THREONINE-PROTEIN KINASE SPRK1
KeywordsTRANSFERASE / SRPK / KINASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CHROMOSOME PARTITION / DIFFERENTIATION / MRNA PROCESSING / MRNA SPLICING / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


sperm DNA condensation / positive regulation of cell-cell adhesion / regulation of mRNA processing / endothelial cell morphogenesis / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / alpha-actinin binding / bicellular tight junction ...sperm DNA condensation / positive regulation of cell-cell adhesion / regulation of mRNA processing / endothelial cell morphogenesis / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / alpha-actinin binding / bicellular tight junction / positive regulation of viral genome replication / Replacement of protamines by nucleosomes in the male pronucleus / RNA splicing / cell periphery / cell projection / chromosome segregation / adherens junction / nuclear matrix / cell-cell junction / cell junction / protein-containing complex assembly / cell surface receptor signaling pathway / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell adhesion / intracellular signal transduction / nuclear speck / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / nucleolus / magnesium ion binding / endoplasmic reticulum / signal transduction / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Unstructured region on MAGI / Unstructured region on MAGI / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...: / Unstructured region on MAGI / Unstructured region on MAGI / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / SRSF protein kinase 1 / Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 / SRSF protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNgo, J.C. / Gullinsgrud, J. / Chakrabarti, S. / Nolen, B. / Aubol, B.E. / Fu, X.-D. / Adams, J.A. / McCammon, J.A. / Ghosh, G.
CitationJournal: Mol.Cell / Year: 2005
Title: Interplay between Srpk and Clk/Sty Kinases in Phosphorylation of the Splicing Factor Asf/Sf2 is Regulated by a Docking Motif in Asf/Sf2
Authors: Ngo, J.C. / Chakrabarti, S. / Ding, J.-H. / Velazquez-Dones, A. / Nolen, B. / Aubol, B.E. / Adams, J.A. / Fu, X.-D. / Ghosh, G.
History
DepositionNov 4, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE SPRK1
B: MEMBRANE-ASSOCIATED GUANYLATE KINASE, WW AND PDZ DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9304
Polymers46,4442
Non-polymers4862
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.680, 78.680, 310.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsTHE PROTEIN IS A MONOMER IN SOLUTION, BUT SINCEIN THIS ENTRY, IT IS COMPLEX WITH A PEPTIDE, THEENTRY IS BEING MARKED AS DIMERIC.FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

-
Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE SPRK1 / SRPK1 / SRPK1A PROTEIN KINASE / SERINE/ARGININE- RICH PROTEIN SPECIFIC KINASE 1 / SR-PROTEIN- ...SRPK1 / SRPK1A PROTEIN KINASE / SERINE/ARGININE- RICH PROTEIN SPECIFIC KINASE 1 / SR-PROTEIN-SPECIFIC KINASE 1 / SFRS PROTEIN KINASE 1


Mass: 45225.598 Da / Num. of mol.: 1 / Fragment: RESIDUES 42-256 AND 474-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q12890, UniProt: Q96SB4*PLUS, EC: 2.7.1.37
#2: Protein/peptide MEMBRANE-ASSOCIATED GUANYLATE KINASE, WW AND PDZ DOMAIN-CONTAINING PROTEIN 1 / ATROPHIN-1-INTERACTING PROTEIN 3 / AIP-3 / BAI1-ASSOCIATED PROTEIN 1 / BAP-1 / MEMBRANE-ASSOCIATED ...ATROPHIN-1-INTERACTING PROTEIN 3 / AIP-3 / BAI1-ASSOCIATED PROTEIN 1 / BAP-1 / MEMBRANE-ASSOCIATED GUANYLATE KINASE INVERTED 1 / MAGI-1 / TRINUCLEOTIDE REPEAT-CONTAINING GENE 19 PROTEIN / WW DOMAIN-CONTAINING PROTEIN 3 / WWP3 / 9-MER PEPTIDE


Mass: 1218.394 Da / Num. of mol.: 1 / Fragment: RESIDUES 1382-1390 / Source method: obtained synthetically
Details: 9 MER PEPTIDE RRRERSPTR BOUND TO A GROOVE FORMED BY THE MAP KINASE INSERT, HELIX AF AND HELIX AG
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q96QZ7
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Compound detailsINVOLVED IN THE REGULATORY NETWORK FOR SPLICING, CONTROLLING THE INTRANUCLEAR DISTRIBUTION OF ...INVOLVED IN THE REGULATORY NETWORK FOR SPLICING, CONTROLLING THE INTRANUCLEAR DISTRIBUTION OF SPLICING FACTORS IN INTERPHASE CELLS AND THE REORGANIZATION OF NUCLEAR SPECKLES DURING MITOSIS
Sequence detailsPROTEIN SEQUENCE FROM NCBI (PROTEIN) ACCESSION NP_003128

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growpH: 7
Details: 100MM SODIUM CITRATE PH5.6, 200MM AMMONIUM ACETATE, 15%PEG3350, 5MM PEPTIDE, 5MM ADP, 10MM MGCL2, pH 7.00
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris1drop
2500 mM1dropNaCl
310 %glycerol1drop
41 mMdithiothreitol1drop
5100 mMsodium citrate1reservoir
6200 mMammonium acetate1reservoir
715 %PEG33501reservoir

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 22765 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 84
Reflection
*PLUS
Num. measured all: 255743 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.86

-
Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WAK

1wak


Resolution: 2.4→28.26 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 384267.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 476 3 %RANDOM
Rwork0.228 ---
obs0.228 15613 67.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7232 Å2 / ksol: 0.319045 e/Å3
Displacement parametersBiso mean: 96.2 Å2
Baniso -1Baniso -2Baniso -3
1-21.3 Å214.59 Å20 Å2
2--21.3 Å20 Å2
3----42.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 31 0 2941
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
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_it8.481.5
X-RAY DIFFRACTIONc_mcangle_it11.442
X-RAY DIFFRACTIONc_scbond_it8.262
X-RAY DIFFRACTIONc_scangle_it10.72.5
LS refinement shellResolution: 2.4→2.55 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.478 1037 -
obs--27.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ALL.PARALL.TOP
X-RAY DIFFRACTION4ACETATE.PARACETATE.TOP
X-RAY DIFFRACTION5ADP.PARADP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more