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- PDB-8poi: Molecular Docking of SPF30 Tudor domain with synthetic inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 8poi
TitleMolecular Docking of SPF30 Tudor domain with synthetic inhibitor 4-(pyridin-2-yl)thiazol-2-amine
ComponentsSurvival of motor neuron-related-splicing factor 30
KeywordsRNA BINDING PROTEIN / tudor domain / complex / inhibitor
Function / homology
Function and homology information


RNA splicing, via transesterification reactions / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / Cajal body / mRNA Splicing - Major Pathway / mRNA processing / nuclear speck / apoptotic process / RNA binding / nucleoplasm ...RNA splicing, via transesterification reactions / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / Cajal body / mRNA Splicing - Major Pathway / mRNA processing / nuclear speck / apoptotic process / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain
Similarity search - Domain/homology
4-pyridin-2-yl-1,3-thiazol-2-amine / Survival of motor neuron-related-splicing factor 30
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBorggraefe, J. / Gaussmann, S. / Sattler, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
Helmholtz Association Germany
German Research Foundation (DFG)SFB 1309 325871075 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Pharmacological perturbation of the phase-separating protein SMNDC1.
Authors: Enders, L. / Siklos, M. / Borggrafe, J. / Gaussmann, S. / Koren, A. / Malik, M. / Tomek, T. / Schuster, M. / Reinis, J. / Hahn, E. / Rukavina, A. / Reicher, A. / Casteels, T. / Bock, C. / ...Authors: Enders, L. / Siklos, M. / Borggrafe, J. / Gaussmann, S. / Koren, A. / Malik, M. / Tomek, T. / Schuster, M. / Reinis, J. / Hahn, E. / Rukavina, A. / Reicher, A. / Casteels, T. / Bock, C. / Winter, G.E. / Hannich, J.T. / Sattler, M. / Kubicek, S.
History
DepositionJul 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Survival of motor neuron-related-splicing factor 30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1132
Polymers6,9361
Non-polymers1771
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, Intermolecular NOE
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Survival of motor neuron-related-splicing factor 30 / 30 kDa splicing factor SMNrp / SMN-related protein / Survival motor neuron domain-containing protein 1


Mass: 6935.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMNDC1, SMNR, SPF30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O75940
#2: Chemical ChemComp-ZTI / 4-pyridin-2-yl-1,3-thiazol-2-amine


Mass: 177.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aromatic
131isotropic12D 1H-13C HSQC aliphatic
141isotropic13D (H)CCH-TOCSY
151isotropic12D NOESY w1-13C-filtered
171isotropic12D NOESY w2-13C-filtered
161isotropic13D NOESY w2-w1-13C filtered

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] SPF30(65-128), 20 mM NA- cmp13, 20 mM NA- sodium phosphate, 50 mM NA- NaCl, 5 mM NA- DTT, 100% D2O
Details: 1mM 15N,13C-SPF30(65-128) + 20mM cmp13 in 20mM NaPi pH 6.5, 50mM NaCl, 5mM DTT, lyophiized and resuspended in D2O
Label: SPF30_cmp13 / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSPF30(65-128)[U-13C; U-15N]1
20 mMcmp13NA-1
20 mMsodium phosphateNA-1
50 mMNaClNA-1
5 mMDTTNA-1
Sample conditionsIonic strength: 70 mM / Label: conditons_D20 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz / Details: H/N/C triple-resonance cryogenic probe

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CARA1.9.1.7Keller and Wuthrichpeak picking
HADDOCKBonvinstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 4

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