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- PDB-2k0a: 1H, 15N and 13C chemical shift assignments for Rds3 protein -

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Basic information

Entry
Database: PDB / ID: 2k0a
Title1H, 15N and 13C chemical shift assignments for Rds3 protein
ComponentsPre-mRNA-splicing factor RDS3
KeywordsMETAL BINDING PROTEIN / zinc finger / topological knot / mRNA processing / mRNA splicing / Nucleus / Spliceosome / RNA BINDING PROTEIN
Function / homology
Function and homology information


U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / spliceosomal complex assembly / spliceosomal complex / mRNA splicing, via spliceosome / response to xenobiotic stimulus / nucleus
Similarity search - Function
PHF5-like / PHF5-like protein
Similarity search - Domain/homology
Pre-mRNA-splicing factor RDS3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsLoening, N. / van Roon, A. / Yang, J. / Nagai, K. / Neuhaus, D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif.
Authors: van Roon, A.M. / Loening, N.M. / Obayashi, E. / Yang, J.C. / Newman, A.J. / Hernandez, H. / Nagai, K. / Neuhaus, D.
History
DepositionJan 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor RDS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5504
Polymers12,3541
Non-polymers1963
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Pre-mRNA-splicing factor RDS3 / Regulator of drug sensitivity 3


Mass: 12353.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: Protein was expressed as an N-terminal Glutathione-S-transferase fusion protein
Gene: RDS3 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q06835
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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 15N T1
1312D 15N T2
1412D 15N NOE
1522D 1H-15N HSQC
1622D 1H-13C HSQC full width
1722D 1H-13C HSQC aromatic
1822D 1H-13C HSQC aliphatic
1922D 1H-1H NOESY
11022D 1H-1H NOESY filtered (15N coupled 1H removed from F2)
11123D HN(CA)CB
11223D CBCA(CO)NH
11323D HNCO
11423D HNHAHB
11523D HBHA(CO)NH
11623D (H)CCH-TOCSY
11723D (H)CCH-TOCSY
11813D HNHB
11923D 1H-15N NOESY
12023D 1H-13C NOESY
12123D HACAHB-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1350 uM [U-98% 15N] Rds3p, 20 mM [U-99% 2H] Tris buffer, 200 mM sodium chloride, 1 mM [U-99% 2H] DTT, 93% H2O/7% D2O93% H2O/7% D2O
2700 uM [U-98% 13C; U-98% 15N] Rds3p, 20 mM [U-99% 2H] Tris buffer, 200 mM sodium chloride, 1 mM [U-99% 2H] DTT, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 uMRds3p[U-98% 15N]1
20 mMTris buffer[U-99% 2H]1
200 mMsodium chloride1
1 mMDTT[U-99% 2H]1
700 uMRds3p[U-98% 13C; U-98% 15N]2
20 mMTris buffer[U-99% 2H]2
200 mMsodium chloride2
1 mMDTT[U-99% 2H]2
Sample conditionsIonic strength: 200 / pH: 7.0 / Pressure: ambient atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospinprocessing
CCPN_analysis1.0.15CCPNdata analysis
ARIA1.1.2Linge, O'Donoghue and Nilgesrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: Aria 1.1.2 (modified to allow use of zinc ions), CNS 1.1, Aria 1.1.2 (modified to allow use of zinc ions), CNS 1.1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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