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- PDB-2f3j: The solution structure of the REF2-I mRNA export factor (residues... -

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Basic information

Entry
Database: PDB / ID: 2f3j
TitleThe solution structure of the REF2-I mRNA export factor (residues 1-155).
ComponentsRNA and export factor binding protein 2
KeywordsTRANSPORT PROTEIN / RRM domain / RBD domain.
Function / homology
Function and homology information


mRNA transport / RNA splicing / spliceosomal complex / mRNA processing / single-stranded DNA binding / RNA binding / cytoplasm
Similarity search - Function
Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / 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 ...Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / 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
Aly/REF export factor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / ARIA protocol (Nilges et al., 1997, J. Mol. Biol. 269, 408-422) used for structure calculation.
AuthorsGolovanov, A.P. / Hautbergue, G.M. / Wilson, S.A. / Lian, L.Y.
CitationJournal: Rna / Year: 2006
Title: The solution structure of REF2-I reveals interdomain interactions and regions involved in binding mRNA export factors and RNA.
Authors: Golovanov, A.P. / Hautbergue, G.M. / Tintaru, A.M. / Lian, L.Y. / Wilson, S.A.
History
DepositionNov 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA and export factor binding protein 2


Theoretical massNumber of molelcules
Total (without water)19,6301
Polymers19,6301
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)14 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA and export factor binding protein 2


Mass: 19630.188 Da / Num. of mol.: 1 / Fragment: RRM Domain (Residues 1 - 155)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Refbp2, Ref2 / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RP / References: UniProt: Q9JJW6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
2322D NOESY
143HSQC-IPAP
NMR detailsText: The protein construct contains 14-residue N-terminal T7 tag (MASMTGGQQMGRDP), and C-terminal tag (LEHHHHHH). The T7 tag is unstructured and is omitted in the coordinate file, where residue ...Text: The protein construct contains 14-residue N-terminal T7 tag (MASMTGGQQMGRDP), and C-terminal tag (LEHHHHHH). The T7 tag is unstructured and is omitted in the coordinate file, where residue numbering starts from residue 1 of REF2-I. Last three residues (LEH) in the coordinate file originate from the beginning of C-terminal tag. The N-terminal domain (1-74) of REF2-I is flexible and is largely unstructured, apart from the region 8-18 which forms a transient helix.

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Sample preparation

Details
Solution-IDContentsSolvent system
113C,15N-REF2-I; 20 mM Na phosphate buffer pH 6.3, 100 mM NaCl, 50 mM L-Arg, 50 mM L-Glu, 5 mM EDTA, 50 mM 2-mercaptoethanol, 10 mM DTT, 95% H2O, 5% D2O.20 mM Na phosphate buffer pH 6.3, 100 mM NaCl, 50 mM L-Arg, 50 mM L-Glu, 5 mM EDTA, 50 mM 2-mercaptoethanol, 10 mM DTT, 95% H2O, 5% D2O.
215N-REF2-I; 20 mM Na phosphate buffer pH 6.3, 100 mM NaCl, 50 mM L-Arg, 50 mM L-Glu, 5 mM EDTA, 50 mM 2-mercaptoethanol, 10 mM DTT, 95% H2O, 5% D2O.20 mM Na phosphate buffer pH 6.3, 100 mM NaCl, 50 mM L-Arg, 50 mM L-Glu, 5 mM EDTA, 50 mM 2-mercaptoethanol, 10 mM DTT, 95% H2O, 5% D2O.
315N,2H-REF2-I; 20 mM Na phosphate buffer pH 6.3, 100 mM NaCl, 50 mM L-Arg, 50 mM L-Glu, 5 mM EDTA, 50 mM 2-mercaptoethanol, 10 mM DTT, 95% H2O, 5% D2O, 5% liquid crystal media made of C12E5 and hexanol.20 mM Na phosphate buffer pH 6.3, 100 mM NaCl, 50 mM L-Arg, 50 mM L-Glu, 5 mM EDTA, 50 mM 2-mercaptoethanol, 10 mM DTT, 95% H2O, 5% D2O, 5% liquid crystal media made of C12E5 and hexanol.
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.126.3ambient 303 K
20.126.3ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipeDelaglio et al.processing
NMRView5.1Johnson and Blevinsdata analysis
ARIA1.1Nilges et al.structure solution
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: ARIA protocol (Nilges et al., 1997, J. Mol. Biol. 269, 408-422) used for structure calculation.
Software ordinal: 1
Details: Residual dipolar couplings were measured in 5% PEG liquid crystal media (C12E5 + hexane, Ruckert and Otting, 2000, J. Am. Chem. Soc. 122, 7793) and used as SANI restraints in ARIA.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 14

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