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- PDB-9qb2: H/ACA RNP protomer of human telomerase dimer -

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Basic information

Entry
Database: PDB / ID: 9qb2
TitleH/ACA RNP protomer of human telomerase dimer
Components
  • (H/ACA ribonucleoprotein complex subunit ...) x 4
  • Telomerase Cajal body protein 1
  • hTR, Human telomerase RNA
KeywordsRNA BINDING PROTEIN / telomerase / H/ACA / RNA-binding protein
Function / homology
Function and homology information


telomere formation via telomerase / box H/ACA scaRNP complex / box H/ACA telomerase RNP complex / protein localization to Cajal body / snoRNA guided rRNA pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / Isomerases; Intramolecular transferases; Transferring other groups ...telomere formation via telomerase / box H/ACA scaRNP complex / box H/ACA telomerase RNP complex / protein localization to Cajal body / snoRNA guided rRNA pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / Isomerases; Intramolecular transferases; Transferring other groups / Cajal body organization / pseudouridine synthesis / telomerase RNA stabilization / snRNA pseudouridine synthesis / box H/ACA snoRNA binding / regulation of telomerase RNA localization to Cajal body / mRNA pseudouridine synthesis / pseudouridine synthase activity / protein carrier chaperone / telomerase RNA localization to Cajal body / telomerase activity / positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / RNA folding chaperone / positive regulation of telomerase RNA localization to Cajal body / positive regulation of double-strand break repair via nonhomologous end joining / sno(s)RNA-containing ribonucleoprotein complex / telomerase holoenzyme complex / telomerase RNA binding / U3 snoRNA binding / rRNA modification in the nucleus and cytosol / positive regulation of double-strand break repair / telomerase holoenzyme complex assembly / Association of TriC/CCT with target proteins during biosynthesis / Telomere Extension By Telomerase / RNA folding / telomere maintenance via telomerase / RNA processing / Cajal body / positive regulation of double-strand break repair via homologous recombination / positive regulation of telomere maintenance via telomerase / positive regulation of DNA repair / mRNA 3'-UTR binding / fibrillar center / rRNA processing / site of double-strand break / protein-folding chaperone binding / histone binding / chromosome, telomeric region / nuclear body / DNA repair / ubiquitin protein ligase binding / protein-containing complex binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily ...: / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / Uncharacterised domain CHP00451 / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / PUA domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / PUA-like superfamily / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / WD domain, G-beta repeat / Translation protein, beta-barrel domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / H/ACA ribonucleoprotein complex subunit DKC1 / Telomerase Cajal body protein 1 / H/ACA ribonucleoprotein complex subunit 3 / H/ACA ribonucleoprotein complex subunit 2 / H/ACA ribonucleoprotein complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsBalch, S. / Sekne, Z. / Franco-Echevarria, E. / Ludzia, P. / Kretsch, R.C. / Sun, W. / Yu, H. / Ghanim, G.E. / Sigurdur, T.R. / Ding, Y. ...Balch, S. / Sekne, Z. / Franco-Echevarria, E. / Ludzia, P. / Kretsch, R.C. / Sun, W. / Yu, H. / Ghanim, G.E. / Sigurdur, T.R. / Ding, Y. / Das, R. / Nguyen, T.H.D.
Funding support United Kingdom, United States, European Union, China, 8items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/19 United Kingdom
Jane Coffin Childs (JCC) Fund United States
European Molecular Biology Organization (EMBO)European Union
Wellcome Trust226015/Z/22/Z United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R35GM122579 United States
Howard Hughes Medical Institute (HHMI) United States
Chinese Scholarship Council202206620047 China
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01102X/1 United Kingdom
CitationJournal: Science / Year: 2025
Title: Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization.
Authors: Sebastian Balch / Zala Sekne / Elsa Franco-Echevarría / Patryk Ludzia / Rachael C Kretsch / Wenqing Sun / Haopeng Yu / George E Ghanim / Sigurdur Thorkelsson / Yiliang Ding / Rhiju Das / ...Authors: Sebastian Balch / Zala Sekne / Elsa Franco-Echevarría / Patryk Ludzia / Rachael C Kretsch / Wenqing Sun / Haopeng Yu / George E Ghanim / Sigurdur Thorkelsson / Yiliang Ding / Rhiju Das / Thi Hoang Duong Nguyen /
Abstract: Telomerase ribonucleoprotein (RNP) synthesizes telomeric repeats at chromosome ends using a telomerase reverse transcriptase (TERT) and a telomerase RNA (hTR in humans). Previous structural work ...Telomerase ribonucleoprotein (RNP) synthesizes telomeric repeats at chromosome ends using a telomerase reverse transcriptase (TERT) and a telomerase RNA (hTR in humans). Previous structural work showed that human telomerase is typically monomeric, containing a single copy of TERT and hTR. Evidence for dimeric complexes exists, although the composition, high-resolution structure, and function remain elusive. Here, we report the cryo-electron microscopy (cryo-EM) structure of a human telomerase dimer bound to telomeric DNA. The structure reveals a 26-subunit assembly and a dimerization interface mediated by the Hinge and ACA box (H/ACA) RNP of telomerase. Premature aging disease mutations map to this interface. Disrupting dimer formation affects RNP assembly, bulk telomerase activity, and telomere maintenance in cells. Our findings address a long-standing enigma surrounding the telomerase dimer and suggest a role for the dimer in telomerase assembly.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: H/ACA ribonucleoprotein complex subunit DKC1
D: H/ACA ribonucleoprotein complex subunit 1
E: H/ACA ribonucleoprotein complex subunit 2
F: H/ACA ribonucleoprotein complex subunit 3
G: H/ACA ribonucleoprotein complex subunit DKC1
H: H/ACA ribonucleoprotein complex subunit 1
I: H/ACA ribonucleoprotein complex subunit 2
J: H/ACA ribonucleoprotein complex subunit 3
K: Telomerase Cajal body protein 1
b: hTR, Human telomerase RNA
B: hTR, Human telomerase RNA


Theoretical massNumber of molelcules
Total (without water)560,53911
Polymers560,53911
Non-polymers00
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

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H/ACA ribonucleoprotein complex subunit ... , 4 types, 8 molecules CGDHEIFJ

#1: Protein H/ACA ribonucleoprotein complex subunit DKC1 / CBF5 homolog / Dyskerin / Nopp140-associated protein of 57 kDa / Nucleolar protein NAP57 / ...CBF5 homolog / Dyskerin / Nopp140-associated protein of 57 kDa / Nucleolar protein NAP57 / Nucleolar protein family A member 4 / snoRNP protein DKC1


Mass: 57779.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Plasmid details: Endogenous
References: UniProt: O60832, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein H/ACA ribonucleoprotein complex subunit 1 / Nucleolar protein family A member 1 / snoRNP protein GAR1


Mass: 22387.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Plasmid details: Endogenous / References: UniProt: Q9NY12
#3: Protein H/ACA ribonucleoprotein complex subunit 2 / Nucleolar protein family A member 2 / snoRNP protein NHP2


Mass: 17226.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Plasmid details: Endogenous / References: UniProt: Q9NX24
#4: Protein H/ACA ribonucleoprotein complex subunit 3 / Nucleolar protein 10 / Nucleolar protein family A member 3 / snoRNP protein NOP10


Mass: 7719.989 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Plasmid details: Endogenous / References: UniProt: Q9NPE3

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Protein / RNA chain , 2 types, 3 molecules KbB

#5: Protein Telomerase Cajal body protein 1 / WD repeat-containing protein 79 / WD40 repeat-containing protein antisense to TP53 gene / WRAP53beta


Mass: 59357.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Plasmid details: Endogenous / References: UniProt: Q9BUR4
#6: RNA chain hTR, Human telomerase RNA


Mass: 145477.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): 293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: GenBank: 1932797

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Details

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

ComponentName: Protomer structure of human telomerase H/ACA RNP lobe / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120.0 mMHEPESC8H18N2O4S1
2150.0 mMSodium ChlorideNaCl1
32.0 mMMagnesium ChlorideMgCl21
40.05 %Igepal CA630(C2H4O)nC14H22O1
51.0 %TrehaloseC12H22O111
61.0 mMDTTC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 45872 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 78 K
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 66992
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2EPU2.13.0.3175RELimage acquisition
4CTFFIND4CTF correction
7Coot0.9.8.1model fitting
8UCSF ChimeraX1.5model fitting
10RELION4initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
14REFMAC5.8model refinement
15Servalcat0.4.70model refinement
Image processingDetails: All images were processed using RELION 4.0, RELION 5.0 and CryoSPARC 4.1.2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1871285
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260466 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8OUE

8oue


Accession code: 8OUE / Source name: PDB / Type: experimental model
RefinementResolution: 3→165.2 Å / Cor.coef. Fo:Fc: 0.969 / SU B: 11.053 / SU ML: 0.197 / ESU R: 0.274
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.2838 --
obs0.2838 243501 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 155.738 Å2
Refinement stepCycle: 1 / Total: 17814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01218627
ELECTRON MICROSCOPYr_bond_other_d00.01615271
ELECTRON MICROSCOPYr_angle_refined_deg1.3431.84826209
ELECTRON MICROSCOPYr_angle_other_deg0.6111.75835460
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.13551661
ELECTRON MICROSCOPYr_dihedral_angle_2_deg2.9635106
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.768102471
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.070.23068
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0218482
ELECTRON MICROSCOPYr_gen_planes_other0.0020.023913
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it16.47410.6746683
ELECTRON MICROSCOPYr_mcbond_other16.47410.6746683
ELECTRON MICROSCOPYr_mcangle_it24.40419.2948331
ELECTRON MICROSCOPYr_mcangle_other24.40319.2988332
ELECTRON MICROSCOPYr_scbond_it18.31520.26511944
ELECTRON MICROSCOPYr_scbond_other18.31520.26511944
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other29.17736.92317879
ELECTRON MICROSCOPYr_long_range_B_refined40.627205.1972611
ELECTRON MICROSCOPYr_long_range_B_other40.627205.1972612
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.035 18079 -
obs--100 %

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