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- EMDB-23439: Tetrahymena telomerase T5D5 structure at 3.8 Angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-23439
TitleTetrahymena telomerase T5D5 structure at 3.8 Angstrom
Map dataTetrahymena telomerase T5D5 structure
Sample
  • Complex: Tetrahymena telomerase T5D5 structure
    • RNA: Telomerase RNATelomerase RNA component
    • DNA: telomere DNA
    • Protein or peptide: Telomerase La-related protein p65
    • Protein or peptide: Telomerase reverse transcriptase
    • Protein or peptide: Telomerase holoenzyme Teb1 subunit
    • Protein or peptide: Telomerase holoenzyme Teb2 subunit
    • Protein or peptide: Telomerase holoenzyme Teb3 subunit
    • Protein or peptide: Telomerase associated protein p50
  • Ligand: ZINC ION
Keywordstelomerase / polymerase / reverse transcriptase / ribonucleoprotein / REPLICATION / REPLICATION-RNA-DNA complex
Function / homology
Function and homology information


telomerase catalytic core complex assembly / telomerase RNA stabilization / telomerase RNA reverse transcriptase activity / DNA replication factor A complex / single-stranded telomeric DNA binding / telomerase RNA binding / telomerase holoenzyme complex / telomeric DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase ...telomerase catalytic core complex assembly / telomerase RNA stabilization / telomerase RNA reverse transcriptase activity / DNA replication factor A complex / single-stranded telomeric DNA binding / telomerase RNA binding / telomerase holoenzyme complex / telomeric DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase / DNA recombination / DNA replication / chromosome, telomeric region / DNA repair / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
Telomerase reverse transcriptase TEN domain / Replication factor A protein 3 / Replication factor A protein 3 / xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. ...Telomerase reverse transcriptase TEN domain / Replication factor A protein 3 / Replication factor A protein 3 / xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / Telomerase ribonucleoprotein complex - RNA binding domain / : / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Replication factor A, C-terminal / Replication factor-A C terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Replication protein A 32 kDa subunit / Replication protein A 14 kDa subunit / Telomeric repeat-binding subunit 1 / Telomerase-associated protein of 50 kDa / Telomerase reverse transcriptase / La-related protein 7 homolog
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHe Y / Wang Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131901 United States
National Science Foundation (NSF, United States)MCB2016540 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
CitationJournal: Nature / Year: 2021
Title: Structures of telomerase at several steps of telomere repeat synthesis.
Authors: Yao He / Yaqiang Wang / Baocheng Liu / Christina Helmling / Lukas Sušac / Ryan Cheng / Z Hong Zhou / Juli Feigon /
Abstract: Telomerase is unique among the reverse transcriptases in containing a noncoding RNA (known as telomerase RNA (TER)) that includes a short template that is used for the processive synthesis of G-rich ...Telomerase is unique among the reverse transcriptases in containing a noncoding RNA (known as telomerase RNA (TER)) that includes a short template that is used for the processive synthesis of G-rich telomeric DNA repeats at the 3' ends of most eukaryotic chromosomes. Telomerase maintains genomic integrity, and its activity or dysregulation are critical determinants of human longevity, stem cell renewal and cancer progression. Previous cryo-electron microscopy structures have established the general architecture, protein components and stoichiometries of Tetrahymena and human telomerase, but our understandings of the details of DNA-protein and RNA-protein interactions and of the mechanisms and recruitment involved remain limited. Here we report cryo-electron microscopy structures of active Tetrahymena telomerase with telomeric DNA at different steps of nucleotide addition. Interactions between telomerase reverse transcriptase (TERT), TER and DNA reveal the structural basis of the determination of the 5' and 3' template boundaries, handling of the template-DNA duplex and separation of the product strand during nucleotide addition. The structure and binding interface between TERT and telomerase protein p50 (a homologue of human TPP1) define conserved interactions that are required for telomerase activation and recruitment to telomeres. Telomerase La-related protein p65 remodels several regions of TER, bridging the 5' and 3' ends and the conserved pseudoknot to facilitate assembly of the TERT-TER catalytic core.
History
DepositionFeb 5, 2021-
Header (metadata) releaseMay 12, 2021-
Map releaseMay 12, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-7lmb
  • Surface level: 0.03
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23439.png

Downloads & links

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Map

FileDownload / File: emd_23439.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTetrahymena telomerase T5D5 structure
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.03
Minimum - Maximum-0.116719544 - 0.19461145
Average (Standard dev.)0.00027365232 (±0.0037649523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z348.160348.160348.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1170.1950.000

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Supplemental data

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Sample components

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Entire : Tetrahymena telomerase T5D5 structure

EntireName: Tetrahymena telomerase T5D5 structure
Components
  • Complex: Tetrahymena telomerase T5D5 structure
    • RNA: Telomerase RNATelomerase RNA component
    • DNA: telomere DNA
    • Protein or peptide: Telomerase La-related protein p65
    • Protein or peptide: Telomerase reverse transcriptase
    • Protein or peptide: Telomerase holoenzyme Teb1 subunit
    • Protein or peptide: Telomerase holoenzyme Teb2 subunit
    • Protein or peptide: Telomerase holoenzyme Teb3 subunit
    • Protein or peptide: Telomerase associated protein p50
  • Ligand: ZINC ION

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Supramolecule #1: Tetrahymena telomerase T5D5 structure

SupramoleculeName: Tetrahymena telomerase T5D5 structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Macromolecule #1: Telomerase RNA

MacromoleculeName: Telomerase RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 50.746984 KDa
SequenceString:
AUACCCGCUU AAUUCAUUCA GAUCUGUAAU AGAACUGUCA UUCAACCCCA AAAAUCUAGU GCUGAUAUAA CCUUCACCAA UUAGGUUCA AAUAAGUGGU AAUGCGGGAC AAAAGACUAU CGACAUUUGA UACACUAUUU AUCAAUGGAU GUCUUAUUUU

GENBANK: GENBANK: AF399707.1

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Macromolecule #2: telomere DNA

MacromoleculeName: telomere DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 6.668261 KDa
SequenceString:
(DG)(DT)(DT)(DG)(DG)(DG)(DG)(DT)(DT)(DG) (DG)(DG)(DG)(DT)(DT)(DG)(DG)(DG)(DG)(DT) (DT)

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Macromolecule #3: Telomerase La-related protein p65

MacromoleculeName: Telomerase La-related protein p65 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 64.207363 KDa
SequenceString: MDEYLENTNL EELEQECFME DYQHEDVVEQ ENHQVDANDI YENQQMNDES QLNQDVKISQ QKEQAVEMIE EQQQNNQDKF KQFQDCMAH ITELNFKRNY QNLTEQSSSN NVVAEELDIK ESLKLQMEYY FCDTNLTHDS YLRGIISKSP KNCVDIKVFL K FNKIQQIL ...String:
MDEYLENTNL EELEQECFME DYQHEDVVEQ ENHQVDANDI YENQQMNDES QLNQDVKISQ QKEQAVEMIE EQQQNNQDKF KQFQDCMAH ITELNFKRNY QNLTEQSSSN NVVAEELDIK ESLKLQMEYY FCDTNLTHDS YLRGIISKSP KNCVDIKVFL K FNKIQQIL KQIQDKQIVS TYGIENQSQK KNHKNYKNQN ATFSKKDLIH LIRDSLKESK ILKVKMDSLK VKRRFPFNLE QA LKNSKQR TLYIDFLPPK CSKQTLVSIF GNFRIININL PLQKNSQLCQ GFAFIEFFSE EEANQALITK NSSIPKELIL LTE KKIGQG SIRIITYKKW QEEKQSFKEL SKNQNEQKNK NMNQSRKASD EFVSIDVEIK QNCLIKIINI PQGTLKAEVV LAVR HLGYE FYCDYIDENS NQINSNKISL STQQQNTAQC SNIQIENNLI QQDQHPQLND LLKEGQAMIR FQNSDEQRLA IQKLL NHNN NKLQIEIRGQ ICDVISTIPE DEEKNYWNYI KFKKNEFRKF FFMKKQQKKQ NITQNYNK

UniProtKB: La-related protein 7 homolog

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Macromolecule #4: Telomerase reverse transcriptase

MacromoleculeName: Telomerase reverse transcriptase / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 133.486938 KDa
SequenceString: MQKINNINNN KQMLTRKEDL LTVLKQISAL KYVSNLYEFL LATEKIVQTS ELDTQFQEFL TTTIIASEQN LVENYKQKYN QPNFSQLTI KQVIDDSIIL LGNKQNYVQQ IGTTTIGFYV EYENINLSRQ TLYSSNFRNL LNIFGEEDFK YFLIDFLVFT K VEQNGYLQ ...String:
MQKINNINNN KQMLTRKEDL LTVLKQISAL KYVSNLYEFL LATEKIVQTS ELDTQFQEFL TTTIIASEQN LVENYKQKYN QPNFSQLTI KQVIDDSIIL LGNKQNYVQQ IGTTTIGFYV EYENINLSRQ TLYSSNFRNL LNIFGEEDFK YFLIDFLVFT K VEQNGYLQ VAGVCLNQYF SVQVKQKKWY KNNFNMNGKA TSNNNQNNAN LSNEKKQENQ YIYPEIQRSQ IFYCNHMGRE PG VFKSSFF NYSEIKKGFQ FKVIQEKLQG RQFINSDKIK PDHPQTIIKK TLLKEYQSKN FSCQEERDLF LEFTEKIVQN FHN INFNYL LKKFCKLPEN YQSLKSQVKQ IVQSENKANQ QSCENLFNSL YDTEISYKQI TNFLRQIIQN CVPNQLLGKK NFKV FLEKL YEFVQMKRFE NQKVLDYICF MDVFDVEWFV DLKNQKFTQK RKYISDKRKI LGDLIVFIIN KIVIPVLRYN FYITE KHKE GSQIFYYRKP IWKLVSKLTI VKLEEENLEK VEEKLIPEDS FQKYPQGKLR IIPKKGSFRP IMTFLRKDKQ KNIKLN LNQ ILMDSQLVFR NLKDMLGQKI GYSVFDNKQI SEKFAQFIEK WKNKGRPQLY YVTLDIKKCY DSIDQMKLLN FFNQSDL IQ DTYFINKYLL FQRNKRPLLQ IQQTNNLNSA MEIEEEKINK KPFKMDNINF PYYFNLKERQ IAYSLYDDDD QILQKGFK E IQSDDRPFIV INQDKPRCIT KDIIHNHLKH ISQYNVISFN KVKFRQKRGI PQGLNISGVL CSFYFGKLEE EYTQFLKNA EQVNGSINLL MRLTDDYLFI SDSQQNALNL IVQLQNCANN NGFMFNDQKI TTNFQFPQED YNLEHFKISV QNECQWIGKS IDMNTLEIK SIQKQTQQEI NQTINVAISI KNLKSQLKNK LRSLFLNQLI DYFNPNINSF EGLCRQLYHH SKATVMKFYP F MTKLFQID LKKSKQYSVQ YGKENTNENF LKDILYYTVE DVCKILCYLQ FEDEINSNIK EIFKNLYSWI MWDIIVSYLK KK KQFKGYL NKLLQKIRKS RFFYLKEGCK SLQLILSQQK YQLNKKELEA IEFIDLNNLI QDIKTLIPKI SAKSNQQNTN

UniProtKB: Telomerase reverse transcriptase

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Macromolecule #5: Telomerase holoenzyme Teb1 subunit

MacromoleculeName: Telomerase holoenzyme Teb1 subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 82.040289 KDa
SequenceString: MKLTKGGSYI LKKVDRKQFY QDEEIVMQIK KILGQKTTDC KQYIKCECID GLGDEALIYF EMLANQNQHL QKNDVIMIQD YLNDKTQND KIVVLVTRFQ FCKASHVQPK TAQKESIQLL NTEKTIIQKS KITKNPAEEV LKFIEVNEKD NSSNSEDMII E QQKQEIKN ...String:
MKLTKGGSYI LKKVDRKQFY QDEEIVMQIK KILGQKTTDC KQYIKCECID GLGDEALIYF EMLANQNQHL QKNDVIMIQD YLNDKTQND KIVVLVTRFQ FCKASHVQPK TAQKESIQLL NTEKTIIQKS KITKNPAEEV LKFIEVNEKD NSSNSEDMII E QQKQEIKN NQKEKQSING FNLEDSYSNI SDITNFGGKS NFNIGSLSDQ LSKQTLLISQ LQVGKNRFSF KFEGRVVYKS ST FQNQQDS KYFFITAQDA NNQEINLSFW QKVDQSYQTL KVGQYYYFIG GEVKQFKNNL ELKFKFGDYQ IIPKETLSAN YVQ PLALQP SKQFGNDSIG DSDYSIHNLI EKEESIAQKG YNGQKNNKYR QNNNNSKHTL LISEVLKTSK QYLSVLAQVV DIQS SDKNI RLKICDNSCN QELKVVIFPD LCYEWRDKFS INKWYYFNEF VRQIYNDEVQ LKNNIHSSIK ESDDQRKVIT YNQEQ GVFK KSISINSNDS FEIKPKISYK NNSNQEQRIY SSIEEIIQQA QASEIGQKKE FYVYGNLVSI QMKNKLYYYR CTCQGK SVL KYHGDSFFCE SCQQFINPQV HLMLRAFVQD STGTIPVMIF DQQSSQLINQ IDPSIHVQEA GQYVKNCIEN GQEEIIR QL FSKLDFARFI FEIQFENKEF NNEQEIAYKV LKIEKENIKE ESKYLLKKLE HLINNNQNN

UniProtKB: Telomeric repeat-binding subunit 1

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Macromolecule #6: Telomerase holoenzyme Teb2 subunit

MacromoleculeName: Telomerase holoenzyme Teb2 subunit / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 30.993035 KDa
SequenceString: MSNRVQGGFD NNSGNNQSAQ KQQAEKIPQI TVPLNCFMIN QIVKAAKENP QAHSGNHYEW YGAFENAIIT AKFEFLQSIN DSPKIMGKL SDSTGCIEVV IQKSKMSDEL PEFVQAYEIE LQNNGNRHKY VRAMLKMRKN AQIQLLYFSI VNDANEISRH G LDLCLRYL ...String:
MSNRVQGGFD NNSGNNQSAQ KQQAEKIPQI TVPLNCFMIN QIVKAAKENP QAHSGNHYEW YGAFENAIIT AKFEFLQSIN DSPKIMGKL SDSTGCIEVV IQKSKMSDEL PEFVQAYEIE LQNNGNRHKY VRAMLKMRKN AQIQLLYFSI VNDANEISRH G LDLCLRYL QRKHGIEDFM HMTNDKAHNN HNASAQKVHY QIDRNQQPKE QVLELMRQIL KHNPNDQIPK SKIIEFFQSQ LN QVQINQI LQQLVSANEI FSVGSDNYLL NV

UniProtKB: Replication protein A 32 kDa subunit

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Macromolecule #7: Telomerase holoenzyme Teb3 subunit

MacromoleculeName: Telomerase holoenzyme Teb3 subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 14.007626 KDa
SequenceString:
MDAEQEQVMY PRILFEQMAQ FRGKKVTVVG NVCNEDQNDS LVIEFGPTGL NQHVVIDNYR RVDLNNTTKF VEIRGVVLNQ NIVSCEELT EFEQKDPFDF DTYSKLIHLS QSDKLSSLFT DQ

UniProtKB: Replication protein A 14 kDa subunit

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Macromolecule #8: Telomerase associated protein p50

MacromoleculeName: Telomerase associated protein p50 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 50.049688 KDa
SequenceString: MKLLLQNQNI FQKLKNTLNG CIKKFYDTYQ DLEQMQKFEM IVEDKLLFRY SCSQSEMFSA QIQAHYLEKR VLQLTDGNVK YIVNFRDKG VLDKANFFDT PNNSLVIIRQ WSYEIYYTKN TFQINLVIDE MRCIDIITTI FYCKLELDFT QGIKGISKSS S FSNQIYEY ...String:
MKLLLQNQNI FQKLKNTLNG CIKKFYDTYQ DLEQMQKFEM IVEDKLLFRY SCSQSEMFSA QIQAHYLEKR VLQLTDGNVK YIVNFRDKG VLDKANFFDT PNNSLVIIRQ WSYEIYYTKN TFQINLVIDE MRCIDIITTI FYCKLELDFT QGIKGISKSS S FSNQIYEY SAQYYKAIQL LKKLLINDSY ISELYNSTKS KQQPRLFIFQ SFKPKMNLAE QNLSRQFEQC QQDDFGDGCL LQ IVNYTHQ SLKQIENKNN SNQIVNGQNE ISKKKRVLKS NEDLYKISLQ KQLKIFQEEE IELHSQSTIR NQTNQQLETF ESD TSKRNS EKILHSINEL NTSKQKVNQM NSSQHQIQKL ENNNLNKNIL NQINENDIKN ELEERQQQHL TQSFNSKAQL KKII TLKKN QDILLFKPQE QEGSKKY

UniProtKB: Telomerase-associated protein of 50 kDa

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120360

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