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- EMDB-52979: Catalytic core 1 of dimeric human telomerase -

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Basic information

Entry
Database: EMDB / ID: EMD-52979
TitleCatalytic core 1 of dimeric human telomerase
Map data
Sample
  • Complex: Catalytic core 1 of dimeric human telomerase
    • Protein or peptide: Telomerase reverse transcriptase
    • RNA: hTR, human telomerase RNA (253-mer)
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*G)-3')
    • Protein or peptide: Adrenocortical dysplasia protein homolog
KeywordsHuman telomerase catalytic core / reverse transcriptase / DNA substrate bound / DNA BINDING PROTEIN
Function / homology
Function and homology information


telomere assembly / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / segmentation / positive regulation of protein localization to nucleolus / siRNA transcription ...telomere assembly / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / segmentation / positive regulation of protein localization to nucleolus / siRNA transcription / urogenital system development / telomerase catalytic core complex / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomerase inhibitor activity / establishment of protein localization to telomere / regulation of establishment of protein localization to telomere / shelterin complex / Telomere C-strand synthesis initiation / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / siRNA processing / telomere maintenance via recombination / telomere capping / positive regulation of vascular associated smooth muscle cell migration / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / telomerase RNA binding / telomerase holoenzyme complex / embryonic limb morphogenesis / protein localization to chromosome, telomeric region / DNA biosynthetic process / RNA-templated transcription / telomeric DNA binding / positive regulation of stem cell proliferation / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / mitochondrial nucleoid / negative regulation of cellular senescence / Telomere Extension By Telomerase / replicative senescence / positive regulation of Wnt signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / telomere maintenance via telomerase / negative regulation of endothelial cell apoptotic process / response to cadmium ion / positive regulation of vascular associated smooth muscle cell proliferation / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / DNA polymerase binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / RNA-directed DNA polymerase activity / skeletal system development / positive regulation of D-glucose import / mitochondrion organization / intracellular protein transport / Formation of the beta-catenin:TCF transactivating complex / telomerase activity / transcription coactivator binding / PML body / DNA Damage/Telomere Stress Induced Senescence / regulation of protein stability / positive regulation of miRNA transcription / RNA-directed DNA polymerase / positive regulation of protein binding / positive regulation of angiogenesis / protein import into nucleus / structural constituent of chromatin / nucleosome / protein-folding chaperone binding / heart development / cellular response to hypoxia / negative regulation of neuron apoptotic process / tRNA binding / chromosome, telomeric region / nuclear speck / nuclear body / protein heterodimerization activity / RNA-directed RNA polymerase activity / protein-containing complex binding / nucleolus / protein homodimerization activity / DNA binding / RNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / : / Shelterin complex subunit, TPP1/ACD / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / : ...Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / : / Shelterin complex subunit, TPP1/ACD / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Histone H2A / Histone H2B / Telomerase reverse transcriptase / Adrenocortical dysplasia protein homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBalch S / Sekne Z / Franco-Echevarria E / Ludzia P / Kretsch RC / Sun W / Yu H / Ghanim GE / Sigurdur TR / Ding Y ...Balch S / Sekne Z / Franco-Echevarria E / Ludzia P / Kretsch RC / Sun W / Yu H / Ghanim GE / Sigurdur TR / Ding Y / Das R / Nguyen THD
Funding support United Kingdom, United States, European Union, China, 8 items
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
Title: CryoEM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization
Authors: Balch S / Sekne Z / Franco-Echevarria E / Ludzia P / Kretsch RC / Sun W / Yu H / Ghanim GE / Sigurdur TR / Ding Y / Das R / Nguyen THD
History
DepositionFeb 28, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52979.png

Downloads & links

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Map

FileDownload / File: emd_52979.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.52 Å		1.06 Å/pix.
x 280 pix.
= 296.52 Å		1.06 Å/pix.
x 280 pix.
= 296.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00859
Minimum - Maximum-0.026344001 - 0.0946981
Average (Standard dev.)0.00023573852 (±0.002117531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52979_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52979_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52979_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Catalytic core 1 of dimeric human telomerase

EntireName: Catalytic core 1 of dimeric human telomerase
Components
  • Complex: Catalytic core 1 of dimeric human telomerase
    • Protein or peptide: Telomerase reverse transcriptase
    • RNA: hTR, human telomerase RNA (253-mer)
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*G)-3')
    • Protein or peptide: Adrenocortical dysplasia protein homolog

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Supramolecule #1: Catalytic core 1 of dimeric human telomerase

SupramoleculeName: Catalytic core 1 of dimeric human telomerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Telomerase reverse transcriptase

MacromoleculeName: Telomerase reverse transcriptase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.195812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPRAPRCRAV RSLLRSHYRE VLPLATFVRR LGPQGWRLVQ RGDPAAFRAL VAQCLVCVPW DARPPPAAPS FRQVSCLKEL VARVLQRLC ERGAKNVLAF GFALLDGARG GPPEAFTTSV RSYLPNTVTD ALRGSGAWGL LLRRVGDDVL VHLLARCALF V LVAPSCAY ...String:
MPRAPRCRAV RSLLRSHYRE VLPLATFVRR LGPQGWRLVQ RGDPAAFRAL VAQCLVCVPW DARPPPAAPS FRQVSCLKEL VARVLQRLC ERGAKNVLAF GFALLDGARG GPPEAFTTSV RSYLPNTVTD ALRGSGAWGL LLRRVGDDVL VHLLARCALF V LVAPSCAY QVCGPPLYQL GAATQARPPP HASGPRRRLG CERAWNHSVR EAGVPLGLPA PGARRRGGSA SRSLPLPKRP RR GAAPEPE RTPVGQGSWA HPGRTRGPSD RGFCVVSPAR PAEEATSLEG ALSGTRHSHP SVGRQHHAGP PSTSRPPRPW DTP CPPVYA ETKHFLYSSG DKEQLRPSFL LSSLRPSLTG ARRLVETIFL GSRPWMPGTP RRLPRLPQRY WQMRPLFLEL LGNH AQCPY GVLLKTHCPL RAAVTPAAGV CAREKPQGSV AAPEEEDTDP RRLVQLLRQH SSPWQVYGFV RACLRRLVPP GLWGS RHNE RRFLRNTKKF ISLGKHAKLS LQELTWKMSV RDCAWLRRSP GVGCVPAAEH RLREEILAKF LHWLMSVYVV ELLRSF FYV TETTFQKNRL FFYRKSVWSK LQSIGIRQHL KRVQLRELSE AEVRQHREAR PALLTSRLRF IPKPDGLRPI VNMDYVV GA RTFRREKRAE RLTSRVKALF SVLNYERARR PGLLGASVLG LDDIHRAWRT FVLRVRAQDP PPELYFVKVD VTGAYDTI P QDRLTEVIAS IIKPQNTYCV RRYAVVQKAA HGHVRKAFKS HVSTLTDLQP YMRQFVAHLQ ETSPLRDAVV IEQSSSLNE ASSGLFDVFL RFMCHHAVRI RGKSYVQCQG IPQGSILSTL LCSLCYGDME NKLFAGIRRD GLLLRLVDDF LLVTPHLTHA KTFLRTLVR GVPEYGCVVN LRKTVVNFPV EDEALGGTAF VQMPAHGLFP WCGLLLDTRT LEVQSDYSSY ARTSIRASLT F NRGFKAGR NMRRKLFGVL RLKCHSLFLD LQVNSLQTVC TNIYKILLLQ AYRFHACVLQ LPFHQQVWKN PTFFLRVISD TA SLCYSIL KAKNAGMSLG AKGAAGPLPS EAVQWLCHQA FLLKLTRHRV TYVPLLGSLR TAQTQLSRKL PGTTLTALEA AAN PALPSD FKTILD

UniProtKB: Telomerase reverse transcriptase

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Molecular weightTheoretical: 14.140584 KDa
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VRRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Molecular weightTheoretical: 18.074932 KDa
SequenceString:
MPDPAKSAPA PKKGSKKAVT KVQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSNPRN LSPTKPGGSE DRQPPPSQLS AIPPFCLVLR A GIAGQV

UniProtKB: Histone H2B

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Macromolecule #6: Adrenocortical dysplasia protein homolog

MacromoleculeName: Adrenocortical dysplasia protein homolog / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.013086 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRCL VTREALDTSD WEEKEFGFR GTEGRLLLLQ DCGVHVQVAE GGAPAEFYLQ VDRFSLLPTE QPRLRVPGCN QDLDVQKKLY DCLEEHLSES T SSNAGLSL ...String:
MAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRCL VTREALDTSD WEEKEFGFR GTEGRLLLLQ DCGVHVQVAE GGAPAEFYLQ VDRFSLLPTE QPRLRVPGCN QDLDVQKKLY DCLEEHLSES T SSNAGLSL SQLLDEMRED QEHQGALVCL AESCLTLEGP CTAPPVTHWA ASRCKATGEA VYTVPSSMLC ISENDQLILS SL GPCQRTQ GPELPPPDPA LQDLSLTLIA SPPSSPSSSG TPALPGHMSS EESGTSISLL PALSLAAPDP GQRSSSQPSP AIC SAPATL TPRSPHASRT PSSPLQSCTP SLSPRSHVPS PHQALVTRPQ KPSLEFKEFV GLPCKNRPPF PRTGATRGAQ EPCS VWEPP KRHRDGSAFQ YEYEPPCTSL CARVQAVRLP PQLMAWALHF LMDAQPGSEP TPM

UniProtKB: Adrenocortical dysplasia protein homolog

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Macromolecule #2: hTR, human telomerase RNA (253-mer)

MacromoleculeName: hTR, human telomerase RNA (253-mer) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 145.477797 KDa
SequenceString: GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU GCCGCCUUCC ACCGUUCAUU C UAGAGCAA ...String:
GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU GCCGCCUUCC ACCGUUCAUU C UAGAGCAA ACAAAAAAUG UCAGCUGCUG GCCCGUUCGC CCCUCCCGGG GACCUGCGGC GGGUCGCCUG CCCAGCCCCC GA ACCCCGC CUGGAGGCCG CGGUCGGCCC GGGGCUUCUC CGGAGGCACC CACUGCCACC GCGAAGAGUU GGGCUCUGUC AGC CGCGGG UCUCUCGGGG GCGAGGGCGA GGUUCAGGCC UUUCAGGCCG CAGGAAGAGG AACGGAGCGA GUCCCCGCGC GCGG CGCGA UUCCCUGAGC UGUGGGACGU GCACCCAGGA CUCGGCUCAC ACAUGC

GENBANK: GENBANK: U85256.1

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Macromolecule #5: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*G)-3')

MacromoleculeName: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*G)-3') / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.193458 KDa
SequenceString:
(DG)(DT)(DT)(DA)(DG)(DG)(DG)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium Chloride
2.0 mMMgCl2Magnesium Chloride
0.05 %(C2H4O)nC14H22OIgepal CA630
1.0 %C12H22O11Trehalose
1.0 mMC4H10O2S2DTT
GridModel: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 8 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 66992 / Average exposure time: 2.5 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 45872 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsAll images were processed using RELION 4.0, RELION 5.0 and CryoSPARC 4.1.2
Particle selectionNumber selected: 1871285
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7qxa

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 138966
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationSoftware - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7qxa


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-9qay:
Catalytic core 1 of dimeric human telomerase

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