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Yorodumi- PDB-5mf9: Solution structure of the RBM5 OCRE domain in complex with polypr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mf9 | |||||||||||||||
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Title | Solution structure of the RBM5 OCRE domain in complex with polyproline SmN peptide. | |||||||||||||||
Components |
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Keywords | SPLICING / OCRE / Poly proline binding domain / SmN / alternative splicing | |||||||||||||||
Function / homology | Function and homology information Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / Cajal body / spliceosomal snRNP assembly / RNA processing / mRNA Splicing - Major Pathway / DNA-templated transcription termination ...Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / Cajal body / spliceosomal snRNP assembly / RNA processing / mRNA Splicing - Major Pathway / DNA-templated transcription termination / spliceosomal complex / cytoplasmic ribonucleoprotein granule / mRNA splicing, via spliceosome / Z disc / snRNP Assembly / nervous system development / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / positive regulation of apoptotic process / axon / negative regulation of cell population proliferation / mRNA binding / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||||||||
Authors | Mourao, A. / Sattler, M. / Bonnal, S. / Komal, S. / Warner, L. / Bordonne, R. / Valcarcel, J. | |||||||||||||||
Funding support | Germany, Spain, 4items
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Citation | Journal: Elife / Year: 2016 Title: Structural basis for the recognition ofspliceosomal SmN B B proteins by theRBM5 OCRE domain in splicing regulation Authors: Mourao, A. / Bonnal, S. / Komal, S. / Warner, L. / Bordonne, R. / Valcarcel, J. / Sattler, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mf9.cif.gz | 248.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mf9.ent.gz | 217.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/5mf9 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/5mf9 | HTTPS FTP |
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-Related structure data
Related structure data | 5mfyC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7436.785 Da / Num. of mol.: 1 / Fragment: UNP residues 451-511 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBM5, H37, LUCA15 / Production host: Escherichia coli (E. coli) / References: UniProt: P52756 |
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#2: Protein/peptide | Mass: 1136.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1, SMN, SMNT, SMN2, SMNC / Production host: Escherichia coli (E. coli) / References: UniProt: Q16637 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solid Contents: 2 mM [U-99% 15N] 15N, 2 mM [U-99% 13C; U-99% 15N] 13C_15N, 2 mM [U-13C; U-15N] unlabel, 90% H2O/10% D2O Label: OCRE_SmN / Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 mM / Label: 15N_sample / pH: 6.5 / Pressure: 1 bar / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |