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- PDB-1mp1: Solution structure of the PWI motif from SRm160 -

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Basic information

Entry
Database: PDB / ID: 1mp1
TitleSolution structure of the PWI motif from SRm160
ComponentsSer/Arg-related nuclear matrix protein
KeywordsRNA BINDING PROTEIN / four helix bundle
Function / homology
Function and homology information


RNA splicing, via transesterification reactions / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / RHOBTB1 GTPase cycle / localization / RHOBTB2 GTPase cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway ...RNA splicing, via transesterification reactions / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / RHOBTB1 GTPase cycle / localization / RHOBTB2 GTPase cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / nuclear matrix / nuclear speck / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
PWI domain / PWI domain / PWI domain superfamily / PWI domain / PWI domain profile. / PWI domain / PWI, domain in splicing factors / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/arginine repetitive matrix protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSzymczyna, B.R. / Bowman, J. / McCracken, S. / Pineda-Lucena, A. / Lu, Y. / Cox, B. / Lambermon, M. / Graveley, B.R. / Arrowsmith, C.H. / Blencowe, B.J.
CitationJournal: Genes Dev. / Year: 2003
Title: Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing.
Authors: Szymczyna, B.R. / Bowman, J. / McCracken, S. / Pineda-Lucena, A. / Lu, Y. / Cox, B. / Lambermon, M. / Graveley, B.R. / Arrowsmith, C.H. / Blencowe, B.J.
History
DepositionSep 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ser/Arg-related nuclear matrix protein


Theoretical massNumber of molelcules
Total (without water)12,8691
Polymers12,8691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ser/Arg-related nuclear matrix protein


Mass: 12869.046 Da / Num. of mol.: 1 / Fragment: PWI motif (residues 27-134)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRm160 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-gold (DE3) / References: UniProt: Q8IYB3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.4mM PWI_motif U-15N,13C, 300mM NaCl, 25 mM phosphate buffer, 1mM DTT, 1mM inhibitor cocktail
Solvent system: 90% H20, 10%D2O
Sample conditionsIonic strength: 300mM NaCl, 25mM phosphate buffer / pH: 7.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: DYANA / Version: 1.5 / Developer: Guntert / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on 3085 NOE-derived distance constraints, 106 dihedral angle restraints, and 44 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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