[English] 日本語
Yorodumi
- PDB-7dd1: Crystal structure of SRPK1 in complex with a peptide inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dd1
TitleCrystal structure of SRPK1 in complex with a peptide inhibitor
Components
  • ARG-GLU-ARG-ALA-ARG-THR-ARG
  • SRSF protein kinase 1,SRSF protein kinase 1
KeywordsTRANSFERASE / RNA splicing / kinase inhibitor / Peptide drug
Function / homology
Function and homology information


protein serine/threonine kinase activity => GO:0004674 / sperm DNA condensation / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / negative regulation of viral genome replication / spliceosomal complex assembly / MAP kinase activity / positive regulation of viral genome replication / viral process / RNA splicing ...protein serine/threonine kinase activity => GO:0004674 / sperm DNA condensation / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / negative regulation of viral genome replication / spliceosomal complex assembly / MAP kinase activity / positive regulation of viral genome replication / viral process / RNA splicing / chromosome segregation / nuclear matrix / regulation of gene expression / 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 / chromatin / magnesium ion binding / endoplasmic reticulum / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
SRSF protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Peptide display vector fth1 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLi, Q.Y. / Yung, K.W.Y. / Ngo, J.C.K.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14122319 Hong Kong
CitationJournal: Iscience / Year: 2021
Title: Protein-Protein Interaction Inhibitor of SRPKs Alters the Splicing Isoforms of VEGF and Inhibits Angiogenesis.
Authors: Li, Q. / Zeng, C. / Liu, H. / Yung, K.W.Y. / Chen, C. / Xie, Q. / Zhang, Y. / Wan, S.W.C. / Mak, B.S.W. / Xia, J. / Xiong, S. / Ngo, J.C.K.
History
DepositionOct 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 29, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SRSF protein kinase 1,SRSF protein kinase 1
B: ARG-GLU-ARG-ALA-ARG-THR-ARG


Theoretical massNumber of molelcules
Total (without water)46,2702
Polymers46,2702
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, MicroScale Thermophoresis (MST) assay also indicates the assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint1 kcal/mol
Surface area17530 Å2
Unit cell
Length a, b, c (Å)75.042, 75.042, 313.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein SRSF protein kinase 1,SRSF protein kinase 1


Mass: 45321.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q96SB4-2, non-specific serine/threonine protein kinase
#2: Protein/peptide ARG-GLU-ARG-ALA-ARG-THR-ARG


Mass: 948.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Peptide display vector fth1 (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 3% PEG 3350, 200mM Ammonium acetata, 100mM Sodium Citrate(pH 5.6), 4mM DTT

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30.03 Å / Num. obs: 32136 / % possible obs: 99.9 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 101.35
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.057 / Num. unique obs: 32136

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WAK

1wak


Resolution: 2.05→30.03 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.146 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1690 5 %RANDOM
Rwork0.1802 ---
obs0.1822 32136 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.45 Å2 / Biso mean: 28.642 Å2 / Biso min: 11.25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.05→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 0 260 3153
Biso mean---37.86 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132963
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172817
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6364008
X-RAY DIFFRACTIONr_angle_other_deg1.3671.5786530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68422.237152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11715537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1661517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
LS refinement shellResolution: 2.054→2.107 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 108 -
Rwork0.195 2337 -
all-2445 -
obs--99.55 %

+
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://pdbjlc1.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