+Open data
-Basic information
Entry | Database: PDB / ID: 7fbr | ||||||
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Title | Solution structure of The first RNA binding domain of Matrin-3 | ||||||
Components | Matrin-3 | ||||||
Keywords | RNA BINDING PROTEIN / RRM / ALS/FTD / nuclear matrix protein / Structural Genomics / PSI-2 / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information heart valve development / blastocyst formation / miRNA binding / ventricular septum development / post-transcriptional regulation of gene expression / activation of innate immune response / nuclear matrix / innate immune response / RNA binding / zinc ion binding ...heart valve development / blastocyst formation / miRNA binding / ventricular septum development / post-transcriptional regulation of gene expression / activation of innate immune response / nuclear matrix / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Muto, Y. / Kobayashi, N. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Biomol.Nmr Assign. / Year: 2022 Title: 1 H, 13 C and 15 N resonance assignments and solution structures of the two RRM domains of Matrin-3. Authors: He, F. / Kuwasako, K. / Takizawa, M. / Takahashi, M. / Tsuda, K. / Nagata, T. / Watanabe, S. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guntert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fbr.cif.gz | 628.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fbr.ent.gz | 526.1 KB | Display | PDB format |
PDBx/mmJSON format | 7fbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fbr_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 7fbr_full_validation.pdf.gz | 517.7 KB | Display | |
Data in XML | 7fbr_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 7fbr_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/7fbr ftp://data.pdbj.org/pub/pdb/validation_reports/fb/7fbr | HTTPS FTP |
-Related structure data
Related structure data | 7fbvC 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: 11351.972 Da / Num. of mol.: 1 / Mutation: S397R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Matr3 Production host: Cell-free gateway cloning vector N-term 8xHis eGFP pCellFree_G03 (others) References: UniProt: Q8K310 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Sample state: isotropic / Type: 3D 13C,15N-SEPARATED NOESY SPECTRA |
-Sample preparation
Details | Type: solution Contents: 1.0 mM [U-99% 13C; U-99% 15N] RNA binding protein, 90% H2O/10% D2O Details: 1mM D-DTT;0.02% NaN3 were used to keep the protein condition Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.0 mM / Component: RNA binding protein / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Details: 20mM D-Tris-HCL (PH7.0); 100mM NaCl; 1mM D-DTT;0.02% NaN3 Ionic strength: 100 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: the structures are based on 2063 NOE-derived distance constrains, 41 main chain dihedral angle constraints based on TALOS program and 7 side chain dihedral constraints based on NOE pattern. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with favorable non-bond energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |