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- PDB-4ch0: RRM domain from C. elegans SUP-12 -

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Basic information

Entry
Database: PDB / ID: 4ch0
TitleRRM domain from C. elegans SUP-12
ComponentsPROTEIN SUP-12, ISOFORM B
KeywordsTRANSCRIPTION / DEVELOPMENT
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / pre-mRNA binding / regulation of locomotion / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / regulation of actin cytoskeleton organization / single-stranded RNA binding / nuclear speck / ribonucleoprotein complex
Similarity search - Function
RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RRM domain-containing protein / RRM domain-containing protein
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodSOLUTION NMR / ARIA1.2
AuthorsAmrane, S. / Mackereth, C.D.
CitationJournal: Nat.Commun. / Year: 2014
Title: Backbone-Independent Nucleic Acid Binding by Splicing Factor Sup-12 Reveals Key Aspects of Molecular Recognition
Authors: Amrane, S. / Rebora, K. / Zniber, I. / Dupuy, D. / Mackereth, C.D.
History
DepositionNov 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2May 4, 2016Group: Atomic model / Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: PROTEIN SUP-12, ISOFORM B


Theoretical massNumber of molelcules
Total (without water)10,8311
Polymers10,8311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 20LOWEST ENERGY AND NO VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein PROTEIN SUP-12, ISOFORM B


Mass: 10831.196 Da / Num. of mol.: 1 / Fragment: RRM DOMAIN, RESIDUES 28 TO 121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Tissue: MUSCLESkeletal muscle / Plasmid: PET-HIS1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSY / References: UniProt: H2L051, UniProt: O45189*PLUS
Sequence detailsTHE SAMPLE CONTAINS AN ADDITIONAL GLY-ALA-MET- AT THE N- TERMINUS FOLLOWING CLEAVAGE BY TEV PROTEASE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-NOESY
22213C-NOESY
NMR detailsText: THE SOLUTION STRUCTURE WAS DETERMINED BY USING TRIPLE RESONANCE NMR SPECTROSCOPY ON 15N- AND 13C,15N- LABELED RRM DOMAIN FROM SUP-12. CHEMICAL SHIFT ASSIGNMENTS ARE FOUND IN BMRB ENTRY 18845.

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Sample preparation

Details
Solution-IDContents
110% WATER/90% D2O
2100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300 mM6.5 1.0 atm298.0 K
2300 mM6.5 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance7001
Bruker AvanceBrukerAvance7002

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Processing

NMR software
NameDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRPIPEstructure solution
SPARKYstructure solution
RefinementMethod: ARIA1.2 / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY AND NO VIOLATIONS
Conformers calculated total number: 20 / Conformers submitted total number: 15

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