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- EMDB-52982: Catalytic core 2 of the telomerase dimer with common particles to... -

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Basic information

Entry
Database: EMDB / ID: EMD-52982
TitleCatalytic core 2 of the telomerase dimer with common particles to both catalytic cores of the dimer
Map data
Sample
  • Complex: Catalytic core 2 of human telomerase dimer from particles common to both catalytic cores of the dimer
    • Protein or peptide: TERT, 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 homolog, TPP1
KeywordsHuman telomerase catalytic core / reverse transcriptase / DNA substrate bound / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBalch S / Sekne Z / Franco-Echevarria E / Ludzia P / Kretsch RC / Sun W / Yu H / Ghanim GE / Thorkelsson SR / Ding Y ...Balch S / Sekne Z / Franco-Echevarria E / Ludzia P / Kretsch RC / Sun W / Yu H / Ghanim GE / Thorkelsson SR / 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: To Be Published
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_52982.png

Downloads & links

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Map

FileDownload / File: emd_52982.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: 0.00976
Minimum - Maximum-0.03766956 - 0.09731815
Average (Standard dev.)0.00021946098 (±0.0026878028)
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_52982_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52982_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52982_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Catalytic core 2 of human telomerase dimer from particles common ...

EntireName: Catalytic core 2 of human telomerase dimer from particles common to both catalytic cores of the dimer
Components
  • Complex: Catalytic core 2 of human telomerase dimer from particles common to both catalytic cores of the dimer
    • Protein or peptide: TERT, 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 homolog, TPP1

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Supramolecule #1: Catalytic core 2 of human telomerase dimer from particles common ...

SupramoleculeName: Catalytic core 2 of human telomerase dimer from particles common to both catalytic cores of the dimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TERT, telomerase reverse transcriptase

MacromoleculeName: TERT, telomerase reverse transcriptase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPRAPRCRAV RSLLRSHYRE VLPLATFVRR LGPQGWRLVQ RGDPAAFRAL VAQCLVCVPW DARPPPAAPS FRQVSCLKEL VARVLQRLCE RGAKNVLAFG FALLDGARGG PPEAFTTSVR SYLPNTVTDA LRGSGAWGLL LRRVGDDVLV HLLARCALFV LVAPSCAYQV ...String:
MPRAPRCRAV RSLLRSHYRE VLPLATFVRR LGPQGWRLVQ RGDPAAFRAL VAQCLVCVPW DARPPPAAPS FRQVSCLKEL VARVLQRLCE RGAKNVLAFG FALLDGARGG PPEAFTTSVR SYLPNTVTDA LRGSGAWGLL LRRVGDDVLV HLLARCALFV LVAPSCAYQV CGPPLYQLGA ATQARPPPHA SGPRRRLGCE RAWNHSVREA GVPLGLPAPG ARRRGGSASR SLPLPKRPRR GAAPEPERTP VGQGSWAHPG RTRGPSDRGF CVVSPARPAE EATSLEGALS GTRHSHPSVG RQHHAGPPST SRPPRPWDTP CPPVYAETKH FLYSSGDKEQ LRPSFLLSSL RPSLTGARRL VETIFLGSRP WMPGTPRRLP RLPQRYWQMR PLFLELLGNH AQCPYGVLLK THCPLRAAVT PAAGVCAREK PQGSVAAPEE EDTDPRRLVQ LLRQHSSPWQ VYGFVRACLR RLVPPGLWGS RHNERRFLRN TKKFISLGKH AKLSLQELTW KMSVRDCAWL RRSPGVGCVP AAEHRLREEI LAKFLHWLMS VYVVELLRSF FYVTETTFQK NRLFFYRKSV WSKLQSIGIR QHLKRVQLRE LSEAEVRQHR EARPALLTSR LRFIPKPDGL RPIVNMDYVV GARTFRREKR AERLTSRVKA LFSVLNYERA RRPGLLGASV LGLDDIHRAW RTFVLRVRAQ DPPPELYFVK VDVTGAYDTI PQDRLTEVIA SIIKPQNTYC VRRYAVVQKA AHGHVRKAFK SHVSTLTDLQ PYMRQFVAHL QETSPLRDAV VIEQSSSLNE ASSGLFDVFL RFMCHHAVRI RGKSYVQCQG IPQGSILSTL LCSLCYGDME NKLFAGIRRD GLLLRLVDDF LLVTPHLTHA KTFLRTLVRG VPEYGCVVNL RKTVVNFPVE DEALGGTAFV QMPAHGLFPW CGLLLDTRTL EVQSDYSSYA RTSIRASLTF NRGFKAGRNM RRKLFGVLRL KCHSLFLDLQ VNSLQTVCTN IYKILLLQAY RFHACVLQLP FHQQVWKNPT FFLRVISDTA SLCYSILKAK NAGMSLGAKG AAGPLPSEAV QWLCHQAFLL KLTRHRVTYV PLLGSLRTAQ TQLSRKLPGT TLTALEAAAN PALPSDFKTI LD

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VRRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
SequenceString:
MPDPAKSAPA PKKGSKKAVT KVQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSNPRNL SPTKPGGSED RQPPPSQLSA IPPFCLVLRA GIAGQV

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Macromolecule #6: Adrenocortical dysplasia homolog, TPP1

MacromoleculeName: Adrenocortical dysplasia homolog, TPP1 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRCL VTREALDTSD WEEKEFGFRG TEGRLLLLQD CGVHVQVAEG GAPAEFYLQV DRFSLLPTEQ PRLRVPGCNQ DLDVQKKLYD CLEEHLSEST SSNAGLSLSQ ...String:
MAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRCL VTREALDTSD WEEKEFGFRG TEGRLLLLQD CGVHVQVAEG GAPAEFYLQV DRFSLLPTEQ PRLRVPGCNQ DLDVQKKLYD CLEEHLSEST SSNAGLSLSQ LLDEMREDQE HQGALVCLAE SCLTLEGPCT APPVTHWAAS RCKATGEAVY TVPSSMLCIS ENDQLILSSL GPCQRTQGPE LPPPDPALQD LSLTLIASPP SSPSSSGTPA LPGHMSSEES GTSISLLPAL SLAAPDPGQR SSSQPSPAIC SAPATLTPRS PHASRTPSSP LQSCTPSLSP RSHVPSPHQA LVTRPQKPSL EFKEFVGLPC KNRPPFPRTG ATRGAQEPCS VWEPPKRHRD GSAFQYEYEP PCTSLCARVQ AVRLPPQLMA WALHFLMDAQ PGSEPTPM

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

MacromoleculeName: hTR, human telomerase RNA (253-mer) / type: rna / ID: 2
Source (natural)Organism: Homo sapiens (human)
SequenceString: GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCCC GCGCGCUGUU UUUCUCGCUG ACUUUCAGCG GGCGGAAAAG CCUCGGCCUG CCGCCUUCCA CCGUUCAUUC UAGAGCAAAC ...String:
GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCCC GCGCGCUGUU UUUCUCGCUG ACUUUCAGCG GGCGGAAAAG CCUCGGCCUG CCGCCUUCCA CCGUUCAUUC UAGAGCAAAC AAAAAAUGUC AGCUGCUGGC CCGUUCGCCC CUCCCGGGGA CCUGCGGCGG GUCGCCUGCC CAGCCCCCGA ACCCCGCCUG GAGGCCGCGG UCGGCCCGGG GCUUCUCCGG AGGCACCCAC UGCCACCGCG AAGAGUUGGG CUCUGUCAGC CGCGGGUCUC UCGGGGGCGA GGGCGAGGUU CAGGCCUUUC AGGCCGCAGG AAGAGGAACG GAGCGAGUCC CCGCGCGCGG CGCGAUUCCC UGAGCUGUGG GACGUGCACC CAGGACUCGG CUCACACAUG C

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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 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GTTAGGG

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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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0)
Details: Common particles between telomerase dimer catalytic cores 1 and 2 were identified using https://github.com/sami-chaaban/starparser. 3D refinement was then performed on shared particles.
Number images used: 41195
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

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