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- EMDB-54921: Cryo-EM structure of the catalytic core of human telomerase at th... -

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Basic information

Entry
Database: EMDB / ID: EMD-54921
TitleCryo-EM structure of the catalytic core of human telomerase at the elongation state of the repeat addition cycle
Map data
Sample
  • Complex: Cryo-EM structure of the catalytic core of human telomerase at the elongation state of the repeat addition cycle
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
    • Protein or peptide: Adrenocortical dysplasia protein homolog
    • RNA: hTR, human telomerase RNA
    • Protein or peptide: Telomerase reverse transcriptase
  • Ligand: 1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
Keywordstelomerase / H/ACA / RNA BINDING PROTEIN
Function / homology
Function and homology information


telomere assembly / positive regulation of hair cycle / template-free RNA nucleotidyltransferase activity / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / segmentation / siRNA transcription / urogenital system development ...telomere assembly / positive regulation of hair cycle / template-free RNA nucleotidyltransferase activity / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / segmentation / siRNA transcription / urogenital system development / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / telomerase inhibitor activity / regulation of establishment of protein localization to telomere / telomerase activity / shelterin complex / Telomere C-strand synthesis initiation / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / siRNA processing / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / telomere maintenance via recombination / positive regulation of vascular associated smooth muscle cell migration / telomere capping / telomerase holoenzyme complex / Polymerase switching on the C-strand of the telomere / telomerase RNA binding / embryonic limb morphogenesis / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / protein localization to chromosome, telomeric region / DNA biosynthetic process / RNA-templated transcription / positive regulation of stem cell proliferation / telomeric repeat DNA binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / negative regulation of cellular senescence / mitochondrial nucleoid / replicative senescence / Telomere Extension By Telomerase / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / response to cadmium ion / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of endothelial cell apoptotic process / positive regulation of Wnt signaling pathway / telomere maintenance via telomerase / positive regulation of vascular associated smooth muscle cell proliferation / DNA polymerase binding / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / positive regulation of D-glucose import across plasma membrane / skeletal system development / mitochondrion organization / intracellular protein transport / regulation of protein stability / Formation of the beta-catenin:TCF transactivating complex / PML body / positive regulation of miRNA transcription / RNA-directed DNA polymerase / DNA Damage/Telomere Stress Induced Senescence / transcription coactivator binding / RNA-directed DNA polymerase activity / 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 H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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: 3.2 Å
AuthorsBalch S / Franco-Echevarria E / Ghanim GE / Kretsch RC / Das R / Nguyen THD / Yu H / Sigurdur TR / Ding Y
Funding support United Kingdom, European Union, United States, 5 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/19 United Kingdom
European Molecular Biology Organization (EMBO)Young Investigator Program AwardEuropean 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
CitationJournal: Nat Commun / Year: 2026
Title: Structures of nucleotide-bound human telomerase at several steps of its telomeric DNA repeat addition cycle.
Authors: Sebastian Balch / Elsa Franco-Echevarría / George E Ghanim / Rachael C Kretsch / Rhiju Das / Thi Hoang Duong Nguyen /
Abstract: In most eukaryotes, the reverse transcriptase telomerase counteracts telomere shortening by processively adding telomeric DNA repeat sequences to chromosome ends. Telomerase activity depends on the ...In most eukaryotes, the reverse transcriptase telomerase counteracts telomere shortening by processively adding telomeric DNA repeat sequences to chromosome ends. Telomerase activity depends on the telomerase reverse transcriptase (TERT) and the telomerase RNA (hTR in humans). Processive telomere elongation is critical for genome stability, and defects in this mechanism are linked to cellular dysfunction and human disease. However, the structural basis for telomerase repeat addition processivity in humans has remained elusive. Here, we present cryo-electron microscopy structures of human telomerase bound to telomeric DNA and an incoming nucleotide, captured at three distinct stages of its repeat addition cycle: initiation, elongation, and pre-termination. Across these states, the TERT active site maintains a conserved architecture that stabilises a short DNA-RNA duplex of constant length of four base-pairs. Beyond the active site, we identify dynamic structural features in both TERT and hTR that facilitate substrate engagement and RNA template repositioning, thereby supporting the synthesis of successive telomeric repeats. Together, these structures provide key insights into how human telomerase achieves its unique processivity to maintain telomere length and genome integrity.
History
DepositionAug 28, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54921.png

Downloads & links

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Map

FileDownload / File: emd_54921.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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.01546955 - 0.03566605
Average (Standard dev.)0.00013937494 (±0.00091385137)
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_54921_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_54921_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_54921_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of the catalytic core of human telomerase at th...

EntireName: Cryo-EM structure of the catalytic core of human telomerase at the elongation state of the repeat addition cycle
Components
  • Complex: Cryo-EM structure of the catalytic core of human telomerase at the elongation state of the repeat addition cycle
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
    • Protein or peptide: Adrenocortical dysplasia protein homolog
    • RNA: hTR, human telomerase RNA
    • Protein or peptide: Telomerase reverse transcriptase
  • Ligand: 1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione

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Supramolecule #1: Cryo-EM structure of the catalytic core of human telomerase at th...

SupramoleculeName: Cryo-EM structure of the catalytic core of human telomerase at the elongation state of the repeat addition cycle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 311 KDa

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Macromolecule #1: Histone H2A

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

UniProtKB: Histone H2A

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Macromolecule #2: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #4: Adrenocortical dysplasia protein homolog

MacromoleculeName: Adrenocortical dysplasia protein homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.013086 KDa
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 #6: Telomerase reverse transcriptase

MacromoleculeName: Telomerase reverse transcriptase / type: protein_or_peptide / ID: 6 / 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: DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')

MacromoleculeName: DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.501092 KDa
SequenceString:
(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)

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Macromolecule #5: hTR, human telomerase RNA

MacromoleculeName: hTR, human telomerase RNA / type: rna / ID: 5 / 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 #7: 1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]...

MacromoleculeName: 1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
type: ligand / ID: 7 / Number of copies: 1 / Formula: A1ACD
Molecular weightTheoretical: 480.195 Da

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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 real images: 56415 / 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: 10615175
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 202390
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
Output model

PDB-9shz:
Cryo-EM structure of the catalytic core of human telomerase at the elongation state of the repeat addition cycle

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