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- PDB-2mgz: Solution structure of RBFOX family ASD-1 RRM and SUP-12 RRM in te... -

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Basic information

Entry
Database: PDB / ID: 2mgz
TitleSolution structure of RBFOX family ASD-1 RRM and SUP-12 RRM in ternary complex with RNA
Components
  • Protein ASD-1, isoform a
  • Protein SUP-12, isoform a
  • RNA (5'-R(*UP*GP*CP*AP*UP*GP*GP*UP*GP*UP*GP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / Solution Structure / Protein-RNA complex / Ternary Complex / RRM (RNA recognition motif) / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / pre-mRNA binding / regulation of alternative mRNA splicing, via spliceosome / regulation of locomotion / pre-mRNA intronic binding / regulation of actin cytoskeleton organization / nervous system development / cell differentiation / single-stranded RNA binding / nuclear speck ...alternative mRNA splicing, via spliceosome / pre-mRNA binding / regulation of alternative mRNA splicing, via spliceosome / regulation of locomotion / pre-mRNA intronic binding / regulation of actin cytoskeleton organization / nervous system development / cell differentiation / single-stranded RNA binding / nuclear speck / ribonucleoprotein complex / mRNA binding / nucleus / cytoplasm
Similarity search - Function
FOX1, RNA recognition motif / : / : / 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 ...FOX1, RNA recognition motif / : / : / 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 / RNA (> 10) / RNA-binding protein ASD-1 / RRM domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsTakahashi, M. / Kuwasako, K. / Unzai, S. / Tsuda, K. / Yoshikawa, S. / He, F. / Kobayashi, N. / Guntert, P. / Shirouzu, M. / Ito, T. ...Takahashi, M. / Kuwasako, K. / Unzai, S. / Tsuda, K. / Yoshikawa, S. / He, F. / Kobayashi, N. / Guntert, P. / Shirouzu, M. / Ito, T. / Tanaka, A. / Yokoyama, S. / Hagiwara, M. / Kuroyanagi, H. / Muto, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing
Authors: Kuwasako, K. / Takahashi, M. / Unzai, S. / Tsuda, K. / Yoshikawa, S. / He, F. / Kobayashi, N. / Guntert, P. / Shirouzu, M. / Ito, T. / Tanaka, A. / Yokoyama, S. / Hagiwara, M. / Kuroyanagi, H. / Muto, Y.
History
DepositionNov 12, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein ASD-1, isoform a
B: Protein SUP-12, isoform a
C: RNA (5'-R(*UP*GP*CP*AP*UP*GP*GP*UP*GP*UP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)26,0443
Polymers26,0443
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Protein ASD-1, isoform a / RNA-binding protein ASD-1


Mass: 10588.028 Da / Num. of mol.: 1 / Fragment: UNP residues 97-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: asd-1, CELE_R74.5, R74.5 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EEW7
#2: Protein Protein SUP-12, isoform a


Mass: 11611.009 Da / Num. of mol.: 1 / Fragment: UNP residues 20-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sup-12, CELE_T22B2.4, T22B2.4 / Production host: Escherichia coli (E. coli) / References: UniProt: O45189
#3: RNA chain RNA (5'-R(*UP*GP*CP*AP*UP*GP*GP*UP*GP*UP*GP*C)-3')


Mass: 3845.303 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D 1H-15N NOESY
1613D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.7 mM [U-99% 13C; U-99% 15N] ASD-1-1, 0.7 mM [U-99% 13C; U-99% 15N] SUP-12-2, 0.7 mM RNA-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMASD-1-1[U-99% 13C; U-99% 15N]1
0.7 mMSUP-12-2[U-99% 13C; U-99% 15N]1
0.7 mMRNA-31
Sample conditionsIonic strength: 0.1 / pH: 5-7 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR softwareName: Amber / Version: 9
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Representative conformer: 1

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