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- PDB-8vrc: Tetrahymena thermophila MLP1 RRM domain -

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Basic information

Entry
Database: PDB / ID: 8vrc
TitleTetrahymena thermophila MLP1 RRM domain
ComponentsLA motif RNA-binding domain protein
KeywordsRNA BINDING PROTEIN / La-motif protein / RNA processing / snRNP binding protein
Function / homology
Function and homology information


RNA processing / ribonucleoprotein complex / RNA binding / nucleus
Similarity search - Function
Protein DCL-like / Protein of unknown function (DUF3223) / Lupus La protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
LA motif RNA-binding domain protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsDonaldson, L.W.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2018-05838 Canada
CitationJournal: To Be Published
Title: NMR structure of the second RNA binding domain from Tetrahymena thermophila Mlp1
Authors: Donaldson, L.W.
History
DepositionJan 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LA motif RNA-binding domain protein


Theoretical massNumber of molelcules
Total (without water)11,3801
Polymers11,3801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein LA motif RNA-binding domain protein


Mass: 11379.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Strain: SB210 / Gene: TTHERM_00384860 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21:DE3 / References: UniProt: Q23RK6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-13C HSQC aliphatic
141isotropic12D 1H-13C HSQC aromatic
151isotropic13D HN(CA)CB
1151isotropic13D CBCA(CO)NH
1141isotropic13D C(CO)NH
1131isotropic13D HBHA(CO)NH
1121isotropic13D HNCO
1111isotropic13D HNCA
1101isotropic13D HN(CA)CO
191isotropic13D 1H-13C NOESY
181isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 20 mM sodium phosphate, 135 mM sodium chloride, 0.8 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O
Details: one sample in H2O was used for the structure determination
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
135 mMsodium chloridenatural abundance1
0.8 mMprotein[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 155 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RosettaBaker laboratoryrefinement
XEASYBartels et al.peak picking
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics21000 structure solutions calculated, 100 chosen for further refinement
simulated annealing3100 structure solutions refined and the 20 best solutions were selected as the final ensemble
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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