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- PDB-2juc: URN1 FF domain yeast -

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Basic information

Entry
Database: PDB / ID: 2juc
TitleURN1 FF domain yeast
ComponentsPre-mRNA-splicing factor URN1
KeywordsUNKNOWN FUNCTION / FF / helical bundle / solution / mRNA processing / mRNA splicing / Nucleus / Spliceosome
Function / homology
Function and homology information


prespliceosome / U1 snRNP / U2-type prespliceosome / mRNA splicing, via spliceosome / RNA binding / nucleus
Similarity search - Function
FF domain / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...FF domain / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-splicing factor URN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsURN1 FF domain yeast
AuthorsBonet, R. / Ramirez-Espain, X. / Macias, M.J.
CitationJournal: Proteins / Year: 2008
Title: Solution structure of the yeast URN1 splicing factor FF domain: Comparative analysis of charge distributions in FF domain structures-FFs and SURPs, two domains with a similar fold.
Authors: Bonet, R. / Ramirez-Espain, X. / Macias, M.J.
History
DepositionAug 21, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor URN1


Theoretical massNumber of molelcules
Total (without water)7,1841
Polymers7,1841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Pre-mRNA-splicing factor URN1 / U2-U5-U6 snRNP / RES complex and NTC-interacting pre-mRNA-splicing factor 1


Mass: 7183.930 Da / Num. of mol.: 1 / Fragment: FF domain (residues 212-266)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: URN1 / Plasmid: petm30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06525

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: URN1 FF domain yeast
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-1H NOESY
1323D 1H-15N NOESY
1433D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM FF protein, 20 mM sodium phosphate, 130 mM sodium chloride, 0.03 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 15N] FF protein, 20 mM sodium phosphate, 130 mM sodium chloride, 0.03 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-100% 13C; U-100% 15N] FF protein, 20 mM sodium phosphate, 130 mM sodium chloride, 0.03 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMFF1
20 mMsodium phosphate1
130 mMsodium chloride1
0.03 %sodium azide1
0.5 mMFF[U-100% 15N]2
20 mMsodium phosphate2
130 mMsodium chloride2
0.03 %sodium azide2
0.5 mMFF[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate3
130 mMsodium chloride3
0.03 %sodium azide3
Sample conditionspH: 5.8 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.processing
CNSBrunger, A.T. et al.refinement
CARAKeller, R. et al.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 15

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