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- PDB-9swn: Cryo-EM structure of yeast telomerase holoenzyme -

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Basic information

Entry
Database: PDB / ID: 9swn
TitleCryo-EM structure of yeast telomerase holoenzyme
Components
  • (Ribonucleases P/MRP protein subunit ...) x 3
  • TLC1 RNA
  • Telomerase reverse transcriptase
  • Telomere elongation protein EST1
  • Telomere replication protein EST3
KeywordsRNA BINDING PROTEIN / Telomerase / Telomerase RNA
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / G-quadruplex DNA formation / nucleolar ribonuclease P complex / ribonuclease MRP complex / DNA/RNA helicase activity / telomerase catalytic core complex / ribonuclease P / telomerase activity / regulation of telomere maintenance via telomerase ...nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / G-quadruplex DNA formation / nucleolar ribonuclease P complex / ribonuclease MRP complex / DNA/RNA helicase activity / telomerase catalytic core complex / ribonuclease P / telomerase activity / regulation of telomere maintenance via telomerase / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / telomerase holoenzyme complex / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / tRNA processing / maturation of 5.8S rRNA / telomeric repeat DNA binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / telomere maintenance via telomerase / telomere maintenance / RNA-directed DNA polymerase / rRNA processing / single-stranded DNA binding / chromosome, telomeric region / viral translational frameshifting / GTPase activity / nucleolus / RNA binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribonuclease P/MRP subunit Pop7, fungi / Telomerase activating protein Est1-like, N-terminal / Telomerase activating protein Est1 / DNA/RNA-binding domain, Est1-type / Est1/Ebs1-like / Est1 DNA/RNA binding domain / Pop1, N-terminal / POPLD domain / Ribonucleases P/MRP protein subunit Pop1 / : ...Ribonuclease P/MRP subunit Pop7, fungi / Telomerase activating protein Est1-like, N-terminal / Telomerase activating protein Est1 / DNA/RNA-binding domain, Est1-type / Est1/Ebs1-like / Est1 DNA/RNA binding domain / Pop1, N-terminal / POPLD domain / Ribonucleases P/MRP protein subunit Pop1 / : / Ribonucleases P/MRP protein subunit POP1, N-terminal / POPLD (NUC188) domain / POP1 C-terminal domain / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / 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. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Telomere elongation protein EST1 / Ribonucleases P/MRP protein subunit POP7 / Ribonucleases P/MRP protein subunit POP1 / Ribonucleases P/MRP protein subunit POP6 / Telomere replication protein EST3 / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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
C: Telomere replication protein EST3
E: Ribonucleases P/MRP protein subunit POP6
G: Telomere elongation protein EST1
F: Ribonucleases P/MRP protein subunit POP7
D: Ribonucleases P/MRP protein subunit POP1
B: TLC1 RNA
A: Telomerase reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)710,30710
Polymers710,1527
Non-polymers1553
Water362
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

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Protein , 3 types, 3 molecules CGA

#1: Protein Telomere replication protein EST3 / Ever shorter telomeres protein 3


Mass: 20577.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EST3, YIL009C-A / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03096
#3: Protein Telomere elongation protein EST1 / Ever shorter telomeres protein 1


Mass: 81920.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EST1, YLR233C, L8083.15 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17214
#7: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 102768.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EST2, YLR318W, L8543.12 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06163, RNA-directed DNA polymerase

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Ribonucleases P/MRP protein subunit ... , 3 types, 3 molecules EFD

#2: Protein Ribonucleases P/MRP protein subunit POP6 / RNA-processing protein POP6 / RNases P/MRP 18.2 kDa subunit


Mass: 18234.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53218, ribonuclease P
#4: Protein Ribonucleases P/MRP protein subunit POP7 / RNA-processing protein POP7 / RNases P/MRP 15.8 kDa subunit


Mass: 15844.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38291, ribonuclease P
#5: Protein Ribonucleases P/MRP protein subunit POP1 / RNA-processing protein POP1 / RNases P/MRP 100.4 kDa subunit


Mass: 100559.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41812, ribonuclease P

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RNA chain , 1 types, 1 molecules B

#6: RNA chain TLC1 RNA


Mass: 370246.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U14595.1

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Non-polymers , 3 types, 5 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

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
1Yeast telomerase holoenzymeCOMPLEX#1-#70MULTIPLE SOURCES
2Yeast telomerase holoenzymeCOMPLEX#1-#71NATURALYeast telomerase holoenzyme consists of protein components: Est2, Est1, Est3, Pop1-6-7, Sm proteins,Ku70/80, and a RNA component TLC1
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Escherichia coli (E. coli)
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
5cryoSPARC4.5CTF 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 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125104 / Symmetry type: POINT
RefinementResolution: 3→233.02 Å / Cor.coef. Fo:Fc: 0.955 / WRfactor Rwork: 0.329 / SU B: 14.45 / SU ML: 0.258 / Average fsc free: 0 / Average fsc overall: 0.8026 / Average fsc work: 0.8026 / ESU R: 0.292
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3294 400326 -
all0.329 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 143.84 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0750.01227173
ELECTRON MICROSCOPYr_bond_other_d0.0010.01622990
ELECTRON MICROSCOPYr_ext_dist_refined_b0.0270.134531
ELECTRON MICROSCOPYr_angle_refined_deg1.3631.82737547
ELECTRON MICROSCOPYr_angle_other_deg0.6491.76153269
ELECTRON MICROSCOPYr_dihedral_angle_1_deg12.1586.743775
ELECTRON MICROSCOPYr_dihedral_angle_2_deg4.9995125
ELECTRON MICROSCOPYr_dihedral_angle_other_2_deg1.7825152
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.032103993
ELECTRON MICROSCOPYr_dihedral_angle_6_deg15.439101003
ELECTRON MICROSCOPYr_chiral_restr0.0870.2034444
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0227503
ELECTRON MICROSCOPYr_gen_planes_other0.0030.025957
ELECTRON MICROSCOPYr_nbd_refined0.2130.24307
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1760.218347
ELECTRON MICROSCOPYr_nbtor_refined0.1810.212282
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0650.211846
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1430.2384
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0480.24
ELECTRON MICROSCOPYr_metal_ion_refined0.4010.22
ELECTRON MICROSCOPYr_paralell_plane_angle_deg9.46186
ELECTRON MICROSCOPYr_mcbond_it4.89113.51610279
ELECTRON MICROSCOPYr_mcbond_other4.89113.51610279
ELECTRON MICROSCOPYr_mcangle_it7.96524.37612833
ELECTRON MICROSCOPYr_mcangle_other7.96524.37812834
ELECTRON MICROSCOPYr_scbond_it5.19115.94316894
ELECTRON MICROSCOPYr_scbond_other5.1915.94316895
ELECTRON MICROSCOPYr_scangle_it8.54728.94424714
ELECTRON MICROSCOPYr_scangle_other8.54728.94524715
ELECTRON MICROSCOPYr_lrange_it14.963235.726136880
ELECTRON MICROSCOPYr_lrange_other14.963235.727136881
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
3-3.0780.847295290.847295290.5350.847
3.078-3.1620.602289080.602289080.6390.602
3.162-3.2540.532281270.532281270.7030.532
3.254-3.3540.484272280.484272280.7440.484
3.354-3.4640.433264950.433264950.7760.433
3.464-3.5860.395255170.395255170.7940.395
3.586-3.7210.355246860.355246860.8210.355
3.721-3.8730.314237790.314237790.8650.314
3.873-4.0450.313227050.313227050.8840.313
4.045-4.2420.319217580.319217580.8950.319
4.242-4.4720.317206560.317206560.9090.317
4.472-4.7430.323196030.323196030.9130.323
4.743-5.070.308183880.308183880.9070.308
5.07-5.4760.299171090.299171090.8940.299
5.476-5.9990.306157450.306157450.8660.306
5.999-6.7060.319142730.319142730.850.319
6.706-7.7420.331125300.331125300.8410.331
7.742-9.480.32106200.32106200.8540.32
9.48-13.3950.26581880.26581880.9050.265
13.395-233.020.24644820.24644820.9730.246

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