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- PDB-5zuh: Solution structure of RRM domain of La protein from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 5zuh
TitleSolution structure of RRM domain of La protein from Trypanosoma brucei
ComponentsRNA binding protein La-like protein
KeywordsRNA BINDING PROTEIN / La motif / RRM domain / RNA-binding / Trypanosoma brucei
Function / homology
Function and homology information


maturation of 5S rRNA / tRNA processing / RNA processing / ribosome biogenesis / ribonucleoprotein complex / mRNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Lupus La protein / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Lupus La protein / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA binding protein La-like protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodSOLUTION NMR / distance geometry
AuthorsShan, F.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270780 China
CitationJournal: Febs J. / Year: 2019
Title: A telomerase subunit homolog La protein from Trypanosoma brucei plays an essential role in ribosomal biogenesis.
Authors: Shan, F. / Mei, S. / Zhang, J. / Zhang, X. / Xu, C. / Liao, S. / Tu, X.
History
DepositionMay 7, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 15, 2019ID: 5ZOM
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA binding protein La-like protein


Theoretical massNumber of molelcules
Total (without water)11,2831
Polymers11,2831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8450 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA binding protein La-like protein


Mass: 11282.726 Da / Num. of mol.: 1 / Fragment: RRM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NIH4

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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 NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] RRM, 200 mM sodium chloride, 20 mM sodium phosphate, 2 mM DTT, 2 mM EDTA, 90% H2O/10% D2O
Label: 13C-15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMRRM[U-13C; U-15N]1
200 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
2 mMDTTnatural abundance1
2 mMEDTAnatural abundance1
Sample conditionsIonic strength: 200 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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