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- PDB-2lsl: Solution structure of the C-terminal domain of Tetrahymena telome... -

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Basic information

Entry
Database: PDB / ID: 2lsl
TitleSolution structure of the C-terminal domain of Tetrahymena telomerase protein p65
ComponentsTelomerase associated protein p65
KeywordsRNA BINDING PROTEIN / Telomerase / p65 / La protein / LARP7 / RRM / Tetrahymena
Function / homology
Function and homology information


telomerase catalytic core complex assembly / telomerase RNA stabilization / telomerase holoenzyme complex / telomerase RNA binding / telomere maintenance via telomerase / chromosome, telomeric region
Similarity search - Function
xRRM domain profile. / La protein, xRRM domain / 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. ...xRRM domain profile. / La protein, xRRM domain / 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
La-related protein 7 homolog / La-related protein 7 homolog
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsSingh, M. / Wang, Z. / Koo, B. / Patel, A. / Cascio, D. / Collins, K. / Feigon, J.
CitationJournal: Mol.Cell / Year: 2012
Title: Structural Basis for Telomerase RNA Recognition and RNP Assembly by the Holoenzyme La Family Protein p65.
Authors: Singh, M. / Wang, Z. / Koo, B.K. / Patel, A. / Cascio, D. / Collins, K. / Feigon, J.
History
DepositionMay 1, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Aug 1, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase associated protein p65


Theoretical massNumber of molelcules
Total (without water)16,1911
Polymers16,1911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Telomerase associated protein p65


Mass: 16191.278 Da / Num. of mol.: 1 / Mutation: delta(421-442)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP65 / Plasmid: pET30 LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6JXI6, UniProt: W7X6T2*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HN(CA)CO
1613D HBHA(CO)NH
1713D H(CCO)NH
1823D (H)CCH-TOCSY
1923D (H)CCH-COSY
11023D 1H-13C NOESY
11113D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
190 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
2100 % [U-100% 2H] D2O, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
90 %H2O-11
10 %D2O-2[U-100% 2H]1
20 mMsodium phosphate-31
50 mMsodium chloride-41
1 mMDTT-51
0.01 %sodium azide-61
100 %D2O-7[U-100% 2H]2
20 mMsodium phosphate-82
50 mMsodium chloride-92
1 mMDTT-102
0.01 %sodium azide-112
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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