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- PDB-1u6f: NMR solution structure of TcUBP1, a single RBD-unit from Trypanos... -

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Basic information

Entry
Database: PDB / ID: 1u6f
TitleNMR solution structure of TcUBP1, a single RBD-unit from Trypanosoma cruzi
ComponentsRNA-binding protein UBP1
KeywordsRNA BINDING PROTEIN / trypanosome / TcUBP1 / mRNA-binding protein / GU-rich RNA
Function / homology
Function and homology information


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-binding protein UBP-1
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsVolpon, L. / D'orso, I. / Frasch, A. / Gehring, K.
CitationJournal: Biochemistry / Year: 2005
Title: NMR Structural Study of TcUBP1, a Single RRM Domain Protein from Trypanosoma cruzi: Contribution of a beta Hairpin to RNA Binding
Authors: Volpon, L. / D'Orso, I. / Young, C.R. / Frasch, A. / Gehring, K.
History
DepositionJul 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 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-binding protein UBP1


Theoretical massNumber of molelcules
Total (without water)15,4271
Polymers15,4271
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 / 100structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein RNA-binding protein UBP1 / TcUBP1


Mass: 15427.367 Da / Num. of mol.: 1 / Fragment: Residues 1-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tcubp-1 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q967R0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY
1323D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM TcUBP1 (GQ), 50 mM Tris-HCl, 50 mM NaCl, 1 mM DTT and 1 mM NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
21.5 mM TcUBP1 (GQ), 50 mM Tris-HCl, 50 mM NaCl, 1 mM DTT and 1 mM NaN3, 100% D2O100% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 7.2 / Pressure: ambient / Temperature: 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 DRXBrukerDRX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
Gifa4Marc-Andr Delsucprocessing
XEASY1.3.13Bartelsdata analysis
TALOS2003.027.13.05Baxrefinement
ARIA1.1Nilgesstructure solution
CNS1.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1545 restraints: 1369 are NOE-derived distance constraints, 122 are dihedral angle restraints and 54 are distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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