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- PDB-9swo: The catalytic core of yeast telomerase holoenzyme -

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Basic information

Entry
Database: PDB / ID: 9swo
TitleThe catalytic core of yeast telomerase holoenzyme
Components
  • TLC1 RNA
  • Telomerase reverse transcriptase
KeywordsRNA BINDING PROTEIN / Telomerase / Telomerase RNA
Function / homology
Function and homology information


telomerase catalytic core complex / telomerase activity / telomerase holoenzyme complex / telomerase RNA binding / telomeric repeat DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase / chromosome, telomeric region / nucleolus / metal ion binding / nucleus
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 (RT) catalytic domain profile.
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHu, H. / Franco-Echevarria, E. / Nguyen, T.H.D.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/19 United Kingdom
European Molecular Biology Organization (EMBO)European Union
CitationJournal: Science / Year: 2026
Title: Cryo-electron microscopy structure of the budding yeast telomerase holoenzyme.
Authors: Hongmiao Hu / Hannah Neumann / Gabriela M Teplitz / Elsa Franco-Echevarría / Pascal Chartrand / Raymund J Wellinger / Thi Hoang Duong Nguyen /
Abstract: Telomerase is a reverse transcriptase that synthesizes telomeric repeats at chromosome ends, safeguarding genome integrity. We present the cryo-electron microscopy structure of the budding yeast ...Telomerase is a reverse transcriptase that synthesizes telomeric repeats at chromosome ends, safeguarding genome integrity. We present the cryo-electron microscopy structure of the budding yeast telomerase, which exhibits substantial divergence from its ciliate and vertebrate counterparts. The structure reveals a stable core formed by telomerase RNA TLC1; the three ever shorter telomere (Est) proteins, Est1, Est2 and Est3; and the Pop1/Pop6/Pop7 complex (Pop1/6/7). TLC1, Est3, and Pop1/6/7 serve critical roles in complex assembly. We identified a zinc finger (ZnF) motif in the telomerase reverse transcriptase (TERT) subunit Est2 that is crucial for telomerase function. Structure prediction suggests the presence of ZnFs in TERT from diverse species. These findings offer insights into the functional organization of yeast telomerase and underscore the evolutionary diversity of telomerase holoenzymes.
History
DepositionOct 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: TLC1 RNA
A: Telomerase reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)473,1044
Polymers473,0152
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain TLC1 RNA


Mass: 370246.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U14595.1
#2: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 102768.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06163, RNA-directed DNA polymerase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1The catalytic core of yeast telomerase holoenzymeCOMPLEX#1-#20NATURAL
2Yeast telomerase catalytic coreCOMPLEX#1-#21NATURALYeast telomerase catalytic core consists of protein component Est2 and RNA component TLC1
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Saccharomyces cerevisiae (brewer's yeast)4932
22Saccharomyces cerevisiae (brewer's yeast)4932
Buffer solutionpH: 8
Details: 150 mM NaCl, 20 mM HEPES NaOH pH 8.0, 2 mM MgCl2, 1% glycerol, 0.05% IGEPAL CA-630, 1 mM DTT, 0.2 mM PMSF
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
220 mMHEPESC8H18N2O4S1
32 mMMagnesium chlorideMgCl21
41 %glycerolC3H8O31
50.05 %Igepal CA-630(C2H4O)nC14H22O1
61 mMDithiothreitolC4H10O2S21
70.2 mMPhenylmethanesulfonyl fluorideC7H7FO2S1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Blot Force: 10 Blot Time: 7.0 s Wait Time: 5 min

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 78 K
Image recordingAverage exposure time: 4.4 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 24936
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2REFMAC5.8.0430model refinement
5CTFFINDCTF correction
10cryoSPARC4.5initial Euler assignment
11cryoSPARC4.5final Euler assignment
12cryoSPARC4.5classification
13cryoSPARC4.53D reconstruction
Image processingDetails: Images were processed using RELION5.0 and cryoSPARC
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1876851
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125104 / Symmetry type: POINT
RefinementResolution: 3.7→3.7 Å / Cor.coef. Fo:Fc: 0.946 / WRfactor Rwork: 0.327 / SU B: 28.486 / SU ML: 0.411 / Average fsc free: 0 / Average fsc overall: 0.7965 / Average fsc work: 0.7965 / ESU R: 0.548
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3265 79584 -
all0.327 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 255.323 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0860.0129721
ELECTRON MICROSCOPYr_bond_other_d00.0168113
ELECTRON MICROSCOPYr_ext_dist_refined_b0.0170.112492
ELECTRON MICROSCOPYr_angle_refined_deg1.1491.82413497
ELECTRON MICROSCOPYr_angle_other_deg0.5781.75118813
ELECTRON MICROSCOPYr_dihedral_angle_1_deg12.2446.9561375
ELECTRON MICROSCOPYr_dihedral_angle_2_deg4.441535
ELECTRON MICROSCOPYr_dihedral_angle_other_2_deg3.212563
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.983101373
ELECTRON MICROSCOPYr_dihedral_angle_6_deg14.06410336
ELECTRON MICROSCOPYr_chiral_restr0.080.2031634
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.029522
ELECTRON MICROSCOPYr_gen_planes_other0.0030.022097
ELECTRON MICROSCOPYr_nbd_refined0.1990.21671
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1680.26670
ELECTRON MICROSCOPYr_nbtor_refined0.1830.24464
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0640.24431
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1530.2155
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0050.21
ELECTRON MICROSCOPYr_paralell_plane_angle_deg8.923669
ELECTRON MICROSCOPYr_mcbond_it11.77720.0993510
ELECTRON MICROSCOPYr_mcbond_other11.77720.0993510
ELECTRON MICROSCOPYr_mcangle_it20.49336.1814384
ELECTRON MICROSCOPYr_mcangle_other20.49136.1964385
ELECTRON MICROSCOPYr_scbond_it11.2332.8646211
ELECTRON MICROSCOPYr_scbond_other11.22932.8696212
ELECTRON MICROSCOPYr_scangle_it19.67159.6319113
ELECTRON MICROSCOPYr_scangle_other19.6759.6349114
ELECTRON MICROSCOPYr_lrange_it43.496459.67549180
ELECTRON MICROSCOPYr_lrange_other43.496459.67749181
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.6-3.6931.61558641.61558640.4281.615
3.693-3.7950.90957550.90957550.5340.909
3.795-3.9050.62955750.62955750.660.629
3.905-4.0250.46454660.46454660.7460.464
4.025-4.1560.35852070.35852070.8060.358
4.156-4.3020.31250860.31250860.8460.312
4.302-4.4640.29248510.29248510.880.292
4.464-4.6470.28847170.28847170.8940.288
4.647-4.8530.27645550.27645550.9080.276
4.853-5.0890.28143130.28143130.9150.281
5.089-5.3640.28541600.28541600.910.285
5.364-5.6890.29738780.29738780.8940.297
5.689-6.0810.31336390.31336390.870.313
6.081-6.5670.32934100.32934100.8490.329
6.567-7.1930.33831100.33831100.8420.338
7.193-8.0390.31328600.31328600.8660.313
8.039-9.2770.2924810.2924810.8950.29
9.277-11.3490.25621280.25621280.9210.256
11.349-15.9960.21516200.21516200.9440.215
15.996-137.520.3529080.3529080.950.352

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