+Open data
-Basic information
Entry | Database: PDB / ID: 2ese | ||||||
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Title | Structure of the SAM domain of Vts1p in complex with RNA | ||||||
Components |
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Keywords | Protein/RNA Complex / protein-RNA complex / shape specific recognition / SAM domain / stem-loop / Protein-RNA Complex COMPLEX | ||||||
Function / homology | Function and homology information flap-structured DNA binding / nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of DNA metabolic process / nuclear-transcribed mRNA catabolic process / P-body / protein transport / mRNA binding / nucleotide binding / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Allain, F.H.T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Authors: Oberstrass, F.C. / Lee, A. / Stefl, R. / Janis, M. / Chanfreau, G. / Allain, F.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ese.cif.gz | 823.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ese.ent.gz | 687 KB | Display | PDB format |
PDBx/mmJSON format | 2ese.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ese_validation.pdf.gz | 392.8 KB | Display | wwPDB validaton report |
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Full document | 2ese_full_validation.pdf.gz | 642.3 KB | Display | |
Data in XML | 2ese_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 2ese_validation.cif.gz | 61.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/2ese ftp://data.pdbj.org/pub/pdb/validation_reports/es/2ese | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 7372.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription |
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#2: Protein | Mass: 11561.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+RIL / References: GenBank: 6324935, UniProt: Q08831*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Details | Contents: 0.8mM Protein, 0.8mM RNA |
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Sample conditions | Ionic strength: 50mM NaCl, 50mM Phosphate-Buffer / pH: 6.5 / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: refined with NOEs, dihedral angles, and residual dipolar couplings | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 20 |