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- PDB-5lgf: Solution structure of the N-terminal domain of Ogataea polymorpha... -

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Basic information

Entry
Database: PDB / ID: 5lgf
TitleSolution structure of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase
ComponentsTelomerase reverse transcriptase
KeywordsTRANSCRIPTION / Telomerase / TERT / TEN domain
Function / homology
Function and homology information


telomerase catalytic core complex / telomerase RNA binding / telomeric DNA binding / telomere maintenance via telomerase / telomerase activity / RNA-directed DNA polymerase / chromosome, telomeric region / metal ion binding
Similarity search - Function
Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Telomerase reverse transcriptase
Similarity search - Component
Biological speciesOgataea polymorpha (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsPolshakov, V.I. / Mantsyzov, A.B. / Efimov, S.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-14-00598 Russian Federation
Citation
Journal: Nucleic Acids Res. / Year: 2018
Title: Structure and function of the N-terminal domain of the yeast telomerase reverse transcriptase.
Authors: Petrova, O.A. / Mantsyzov, A.B. / Rodina, E.V. / Efimov, S.V. / Hackenberg, C. / Hakanpaa, J. / Klochkov, V.V. / Lebedev, A.A. / Chugunova, A.A. / Malyavko, A.N. / Zatsepin, T.S. / Mishin, A. ...Authors: Petrova, O.A. / Mantsyzov, A.B. / Rodina, E.V. / Efimov, S.V. / Hackenberg, C. / Hakanpaa, J. / Klochkov, V.V. / Lebedev, A.A. / Chugunova, A.A. / Malyavko, A.N. / Zatsepin, T.S. / Mishin, A.V. / Zvereva, M.I. / Lamzin, V.S. / Dontsova, O.A. / Polshakov, V.I.
#1: Journal: Biomol NMR Assign / Year: 2016
Title: NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase.
Authors: Polshakov, V.I. / Petrova, O.A. / Parfenova, Y.Y. / Efimov, S.V. / Klochkov, V.V. / Zvereva, M.I. / Dontsova, O.A.
History
DepositionJul 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.4Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.5May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.6May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)18,5851
Polymers18,5851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Telomerase reverse transcriptase


Mass: 18584.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ogataea polymorpha (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4IT35

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC aliphatic
133isotropic12D 1H-13C HSQC aromatic
142isotropic13D HNCO
152isotropic13D HCACO
162isotropic13D HNCA
172isotropic13D HN(CO)CA
182isotropic13D HN(CA)CB
192isotropic13D CBCA(CO)NH
1102isotropic13D HBHA(CO)NH
1112isotropic13D HBHANH
1121isotropic13D HNHA
1131isotropic13D HNHB
1141isotropic13D 1H-15N TOCSY
1151isotropic13D 1H-15N NOESY
1163isotropic13D 1H-13C NOESY
1171isotropic12D 1H-15N HSQC
1183isotropic13D (H)CCH-TOCSY
1204isotropic22D DQF-COSY
1214isotropic22D 1H-1H NOESY
1221isotropic11H-15N NOE
1231isotropic115N T1
1241anisotropic115N T2

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 15N] N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution30.5 mM [U-99% 13C; U-99% 15N] N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.02 % sodium azide, 100% D2O13C_15N_sample_D2O100% D2O
solution41.0 mM N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.02 % sodium azide, 100% D2Ounlabled_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMN-terminal domain of Ogataea polymorpha telomerase reverse transcriptase[U-99% 15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
0.02 %sodium azidenatural abundance1
0.5 mMN-terminal domain of Ogataea polymorpha telomerase reverse transcriptase[U-99% 13C; U-99% 15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
0.02 %sodium azidenatural abundance2
0.5 mMN-terminal domain of Ogataea polymorpha telomerase reverse transcriptase[U-99% 13C; U-99% 15N]3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
0.02 %sodium azidenatural abundance3
1.0 mMN-terminal domain of Ogataea polymorpha telomerase reverse transcriptasenatural abundance4
20 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
1 mMDTTnatural abundance4
0.02 %sodium azidenatural abundance4
Sample conditionsIonic strength: 0.05 M / Label: conditions_1 / pH: 7 / PH err: 0.02 / Pressure: 1 atm / Temperature: 303 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE7001Cryo quadro resonance (1H, 13C, 15N, 31P) probe
Bruker AVANCEBrukerAVANCE6002Triple resonance (1H, 13C, 15N) probe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
AutoAssignZimmerman, Moseley, Kulikowski and Montelionedata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
NMRestPolshakovdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RelaxFitPolshakovdata analysis
Insight IIAccelrys Software Inc.data analysis
PROCHECK / PROCHECK-NMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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