+Open data
-Basic information
Entry | Database: PDB / ID: 7z27 | ||||||
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Title | Crystal structure of the SPOC domain of human RBM15 | ||||||
Components | RNA-binding protein 15 | ||||||
Keywords | TRANSCRIPTION / Spoc domain / Rbm15 | ||||||
Function / homology | Function and homology information thrombopoietin-mediated signaling pathway / positive regulation of transcription of Notch receptor target / RNA N6-methyladenosine methyltransferase complex / negative regulation of myeloid cell differentiation / RNA methylation / regulation of megakaryocyte differentiation / placenta blood vessel development / dosage compensation by inactivation of X chromosome / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis ...thrombopoietin-mediated signaling pathway / positive regulation of transcription of Notch receptor target / RNA N6-methyladenosine methyltransferase complex / negative regulation of myeloid cell differentiation / RNA methylation / regulation of megakaryocyte differentiation / placenta blood vessel development / dosage compensation by inactivation of X chromosome / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / regulation of alternative mRNA splicing, via spliceosome / spleen development / nuclear membrane / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Grishkovskaya, I. / Appel, L.M. / Djinovic-Carugo, K. / Slade, D. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators. Authors: Appel, L.M. / Franke, V. / Benedum, J. / Grishkovskaya, I. / Strobl, X. / Polyansky, A. / Ammann, G. / Platzer, S. / Neudolt, A. / Wunder, A. / Walch, L. / Kaiser, S. / Zagrovic, B. / ...Authors: Appel, L.M. / Franke, V. / Benedum, J. / Grishkovskaya, I. / Strobl, X. / Polyansky, A. / Ammann, G. / Platzer, S. / Neudolt, A. / Wunder, A. / Walch, L. / Kaiser, S. / Zagrovic, B. / Djinovic-Carugo, K. / Akalin, A. / Slade, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z27.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z27.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 7z27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z27_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 7z27_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | 7z27_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 7z27_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/7z27 ftp://data.pdbj.org/pub/pdb/validation_reports/z2/7z27 | HTTPS FTP |
-Related structure data
Related structure data | 7z1kSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20118.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBM15, OTT, OTT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T37 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium malonate dibasic monohydrate, 0.1M Bis-Tris propane 6.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→57.45 Å / Num. obs: 62616 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.116 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.45→1.47 Å / Rmerge(I) obs: 2.08 / Num. unique obs: 4578 / CC1/2: 0.571 / Rrim(I) all: 2.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7Z1K Resolution: 1.45→57.45 Å / SU ML: 0.1762 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0172 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→57.45 Å
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Refine LS restraints |
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LS refinement shell |
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