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- PDB-4cio: RRM domain from C. elegans SUP-12 bound to GGUGUGC RNA -

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Basic information

Entry
Database: PDB / ID: 4cio
TitleRRM domain from C. elegans SUP-12 bound to GGUGUGC RNA
Components
  • 5'-R(*GP*GP*UP*GP*UP*GP*CP)-3'
  • PROTEIN SUP-12, ISOFORM A
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / MUSCLE / 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
RNA / 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
DepositionDec 12, 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 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN SUP-12, ISOFORM A
B: 5'-R(*GP*GP*UP*GP*UP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)13,0852
Polymers13,0852
Non-polymers00
Water00
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 / 125LOWEST ENERGY
RepresentativeModel #8

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Components

#1: Protein PROTEIN SUP-12, ISOFORM A / SUP-12


Mass: 10831.196 Da / Num. of mol.: 1 / Fragment: RRM DOMAIN, RESIDUES 28-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Plasmid: PET-HIS1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSY / References: UniProt: O45189
#2: RNA chain 5'-R(*GP*GP*UP*GP*UP*GP*CP)-3'


Mass: 2253.379 Da / Num. of mol.: 1 / Fragment: SUP-12 BINDING MOTIF / Source method: obtained synthetically
Details: THE HEPTAMER SEQUENCE IS DERIVED FROM THE INTRON BETWEEN EXONS 4 AND 5B FROM THE C. ELEGANS EGL-15 GENE.
Source: (synth.) CAENORHABDITIS ELEGANS (invertebrata)
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
11115C-NOESY
121DOUBLE-FILTERED 1H
1311H-TOCSY
141DOUBLE- FILTERED 1H
1511H-NOESY
161HALF- FILTERED 1H
1711H-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED BY USING MULTI- DIMENSIONAL NMR SPECTRSOCOPY WITH 15N-, 13C,15N-, OR 2H- LABELED SUP-12 IN COMPLEX WITH A NATURAL ABUNDANCE GGUGUGC RNA LIGAND. THE CHEMICAL SHIFTS ...Text: THE STRUCTURE WAS DETERMINED BY USING MULTI- DIMENSIONAL NMR SPECTRSOCOPY WITH 15N-, 13C,15N-, OR 2H- LABELED SUP-12 IN COMPLEX WITH A NATURAL ABUNDANCE GGUGUGC RNA LIGAND. THE CHEMICAL SHIFTS HAVE BEEN DEPOSITED PREVIOUSLY IN THE BMRB AS ENTRY 18846.

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Sample preparation

DetailsContents: 100% D2O
Sample conditionsIonic strength: 300 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,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 / Conformers calculated total number: 125 / Conformers submitted total number: 15

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