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Yorodumi- PDB-2mkc: Cooperative Structure of the Heterotrimeric pre-mRNA Retention an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mkc | ||||||
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Title | Cooperative Structure of the Heterotrimeric pre-mRNA Retention and Splicing Complex | ||||||
Components |
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Keywords | SPLICING / spliceosome / Snu17p / Bud13p / Pml1p / heterotrimer / cooperativity / RES / RRM / PROTEIN BINDING / Ist3p | ||||||
Function / homology | Function and homology information maintenance of RNA location / RES complex / generation of catalytic spliceosome for first transesterification step / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / spliceosomal complex assembly / mRNA export from nucleus / spliceosomal complex ...maintenance of RNA location / RES complex / generation of catalytic spliceosome for first transesterification step / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / spliceosomal complex assembly / mRNA export from nucleus / spliceosomal complex / mRNA splicing, via spliceosome / mRNA binding / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Wysoczanski, P. / Schneider, C. / Xiang, S. / Munari, F. / Trowitzsch, S. / Wahl, M.C. / Luhrmann, R. / Becker, S. / Zweckstetter, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex. Authors: Wysoczanski, P. / Schneider, C. / Xiang, S. / Munari, F. / Trowitzsch, S. / Wahl, M.C. / Luhrmann, R. / Becker, S. / Zweckstetter, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mkc.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mkc.ent.gz | 905.7 KB | Display | PDB format |
PDBx/mmJSON format | 2mkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/2mkc ftp://data.pdbj.org/pub/pdb/validation_reports/mk/2mkc | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13495.979 Da / Num. of mol.: 1 / Fragment: UNP residues 25-138 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: IST3, SNU17, YIB5W, YIR005W / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40565 |
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#2: Protein/peptide | Mass: 2514.782 Da / Num. of mol.: 1 / Fragment: UNP residues 22-42 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PML1, YLR016C, L1591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07930 |
#3: Protein/peptide | Mass: 3828.191 Da / Num. of mol.: 1 / Fragment: UNP residues 215-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: BUD13, CWC26, SLC7, YGL174W, G1642 / Production host: Escherichia coli (E. coli) / References: UniProt: P46947 |
Compound details | AUTHORS STATE THAT THE ISOTOPICALLY LABELLED BIOSYNTHETIC PEPTIDES HAVE GS CLONING ARTIFACT AT THE ...AUTHORS STATE THAT THE ISOTOPICAL |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 6.8 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: WATER REFINEMENT (RECOORD) | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 4105 / NOE intraresidue total count: 769 / NOE long range total count: 1597 / NOE medium range total count: 775 / NOE sequential total count: 964 / Hydrogen bond constraints total count: 50 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 115 / Protein psi angle constraints total count: 115 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.62 ° / Conformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 3.2 ° / Maximum upper distance constraint violation: 0.307 Å / Torsion angle constraint violation method: CNS | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0101 Å / Distance rms dev error: 0.0008 Å |