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- PDB-6q44: Est3 telomerase subunit in the yeast Hansenula polymorpha -

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Basic information

Entry
Database: PDB / ID: 6q44
TitleEst3 telomerase subunit in the yeast Hansenula polymorpha
ComponentsUncharacterized protein
KeywordsPROTEIN BINDING / Telomerase / Est3 / OB-fold
Function / homologyShelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / telomerase holoenzyme complex / telomeric DNA binding / telomere maintenance via telomerase / chromosome, telomeric region / Telomere replication protein EST3
Function and homology information
Biological speciesOgataea parapolymorpha DL-1 (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsMantsyzov, A.B. / Mariasina, S.S. / Petrova, O.A. / Efimov, S.V. / Dontsova, O.A. / Polshakov, V.I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-14-00598 Russian Federation
Citation
Journal: Sci Rep / Year: 2020
Title: Insights into the structure and function of Est3 from the Hansenula polymorpha telomerase.
Authors: Shepelev, N.M. / Mariasina, S.S. / Mantsyzov, A.B. / Malyavko, A.N. / Efimov, S.V. / Petrova, O.A. / Rodina, E.V. / Zvereva, M.I. / Dontsova, O.A. / Polshakov, V.I.
#1: Journal: Biomol.Nmr Assign. / Year: 2018
Title: Chemical shift assignments and the secondary structure of the Est3 telomerase subunit in the yeast Hansenula polymorpha.
Authors: Mariasina, S.S. / Efimov, S.V. / Petrova, O.A. / Rodina, E.V. / Malyavko, A.N. / Zvereva, M.I. / Klochkov, V.V. / Dontsova, O.A. / Polshakov, V.I.
History
DepositionDec 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)20,4801
Polymers20,4801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12220 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1rmsd

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Components

#1: Protein Uncharacterized protein


Mass: 20480.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ogataea parapolymorpha DL-1 (fungus) / Gene: HPODL_02192 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W1QJK4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-13C NOESY
123isotropic23D 1H-15N NOESY
133isotropic12D 1H-15N HSQC
141isotropic22D 1H-13C HSQC aliphatic
151isotropic22D 1H-13C HSQC aromatic
184isotropic22D DQF-COSY
174isotropic22D 1H-1H NOESY
162isotropic23D HNCO
1132isotropic23D HN(CO)CA
1122isotropic23D HNCA
1112isotropic23D HN(CA)CB
1102isotropic23D CBCA(CO)NH
193isotropic2HNHA
1163isotropic2HNHB
1151isotropic23D (H)CCH-TOCSY
1141isotropic22D HBCB(CGCD)HD
1191isotropic22D HBCB(CGCDCE)HE
1183isotropic23D 1H-15N TOCSY
1173isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 13C; U-99% 15N] Est3, 100 mM KCl, 50 mM sodium phosphate, 3 mM DTT, 2 % sodium azide, 100% D2O13C; 15N D2O100% D2O
solution20.7 mM [U-99% 13C; U-99% 15N] Est3, 100 mM KCl, 50 mM sodium phosphate, 3 mM DTT, 2 % sodium azide, 90% H2O/10% D2O13C; 15N H2O/D2O90% H2O/10% D2O
solution30.8 mM [U-99% 15N] Est3, 100 mM KCl, 50 mM sodium phosphate, 3 mM DTT, 2 % sodium azide, 90% H2O/10% D2O15N H2O/D2O90% H2O/10% D2O
solution41 mM Est3, 100 mM KCl, 50 mM sodium phosphate, 3 mM DTT, 2 % sodium azide, 100% D2OUnl100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMEst3[U-99% 13C; U-99% 15N]1
100 mMKClnatural abundance1
50 mMsodium phosphatenatural abundance1
3 mMDTTnatural abundance1
2 %sodium azidenatural abundance1
0.7 mMEst3[U-99% 13C; U-99% 15N]2
100 mMKClnatural abundance2
50 mMsodium phosphatenatural abundance2
3 mMDTTnatural abundance2
2 %sodium azidenatural abundance2
0.8 mMEst3[U-99% 15N]3
100 mMKClnatural abundance3
50 mMsodium phosphatenatural abundance3
3 mMDTTnatural abundance3
2 %sodium azidenatural abundance3
1 mMEst3natural abundance4
100 mMKClnatural abundance4
50 mMsodium phosphatenatural abundance4
3 mMDTTnatural abundance4
2 %sodium azidenatural abundance4
Sample conditionsIonic strength: 150 mM / Label: Est3 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Equipped with triple resonance (1H, 13C, 15N) probe
Bruker AVANCE IIIBrukerAVANCE III7002Equipped with quadruple resonance (1H, 13C, 15N, 31P) CryoProbe

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: rmsd
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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