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- EMDB-31811: catalytic core of human telomerase holoenzyme -

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Basic information

Entry
Database: EMDB / ID: EMD-31811
Titlecatalytic core of human telomerase holoenzyme
Map data
Sample
  • Complex: Catalytic core
    • Protein or peptide: Telomerase reverse transcriptase
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • RNA: Telomerase RNA component
    • DNA: Primer DNA
KeywordsTelomerase / REPLICATION
Function / homology
Function and homology information


positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / RNA-templated DNA biosynthetic process ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / nuclear telomere cap complex / siRNA processing / telomere maintenance via recombination / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / RNA-templated transcription / DNA biosynthetic process / telomeric DNA binding / positive regulation of stem cell proliferation / 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 / RNA-directed DNA polymerase activity / negative regulation of endothelial cell apoptotic process / protein localization to CENP-A containing chromatin / response to cadmium ion / CENP-A containing nucleosome / Packaging Of Telomere Ends / positive regulation of vascular associated smooth muscle cell proliferation / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / RNA Polymerase I Promoter Opening / positive regulation of nitric-oxide synthase activity / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / chloroplast / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / positive regulation of D-glucose import / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / mitochondrion organization / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / NoRC negatively regulates rRNA expression / regulation of protein stability / PML body / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / positive regulation of miRNA transcription / RNA-directed DNA polymerase / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / telomerase activity / Transcriptional regulation of granulopoiesis / HCMV Early Events / protein import into nucleus / positive regulation of angiogenesis / structural constituent of chromatin / positive regulation of protein binding / UCH proteinases / nucleosome / heterochromatin formation / chromatin organization / protein-folding chaperone binding / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / heart development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / small ribosomal subunit rRNA binding / Oxidative Stress Induced Senescence
Similarity search - Function
: / 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 H2A, C-terminal domain / C-terminus of histone H2A ...: / 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 H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Translation elongation factor EF1B/ribosomal protein S6 / Histone-fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Telomerase reverse transcriptase / Small ribosomal subunit protein bS6c alpha / Histone H2A type 1-B/E
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsWan F / Ding Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2021
Title: Zipper head mechanism of telomere synthesis by human telomerase.
Authors: Futang Wan / Yongbo Ding / Yuebin Zhang / Zhenfang Wu / Shaobai Li / Lin Yang / Xiangyu Yan / Pengfei Lan / Guohui Li / Jian Wu / Ming Lei /
Abstract: Telomerase, a multi-subunit ribonucleoprotein complex, is a unique reverse transcriptase that catalyzes the processive addition of a repeat sequence to extend the telomere end using a short fragment ...Telomerase, a multi-subunit ribonucleoprotein complex, is a unique reverse transcriptase that catalyzes the processive addition of a repeat sequence to extend the telomere end using a short fragment of its own RNA component as the template. Despite recent structural characterizations of human and Tetrahymena telomerase, it is still a mystery how telomerase repeatedly uses its RNA template to synthesize telomeric DNA. Here, we report the cryo-EM structure of human telomerase holoenzyme bound with telomeric DNA at resolutions of 3.5 Å and 3.9 Å for the catalytic core and biogenesis module, respectively. The structure reveals that a leucine residue Leu980 in telomerase reverse transcriptase (TERT) catalytic subunit functions as a zipper head to limit the length of the short primer-template duplex in the active center. Moreover, our structural and computational analyses suggest that TERT and telomerase RNA (hTR) are organized to harbor a preformed active site that can accommodate short primer-template duplex substrates for catalysis. Furthermore, our findings unveil a double-fingers architecture in TERT that ensures nucleotide addition processivity of human telomerase. We propose that the zipper head Leu980 is a structural determinant for the sequence-based pausing signal of DNA synthesis that coincides with the RNA element-based physical template boundary. Functional analyses unveil that the non-glycine zipper head plays an essential role in both telomerase repeat addition processivity and telomere length homeostasis. In addition, we also demonstrate that this zipper head mechanism is conserved in all eukaryotic telomerases. Together, our study provides an integrated model for telomerase-mediated telomere synthesis.
History
DepositionAug 24, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31811.png

Downloads & links

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Map

FileDownload / File: emd_31811.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 416 pix.
= 457.6 Å		1.1 Å/pix.
x 416 pix.
= 457.6 Å		1.1 Å/pix.
x 416 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-7.028521 - 13.773585000000001
Average (Standard dev.)0.008262343 (±0.24159653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Catalytic core

EntireName: Catalytic core
Components
  • Complex: Catalytic core
    • Protein or peptide: Telomerase reverse transcriptase
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • RNA: Telomerase RNA component
    • DNA: Primer DNA

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Supramolecule #1: Catalytic core

SupramoleculeName: Catalytic core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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
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 #2: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.034355 KDa
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #3: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.790018 KDa
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Small ribosomal subunit protein bS6c alpha

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Macromolecule #4: Telomerase RNA component

MacromoleculeName: Telomerase RNA component / type: rna / ID: 4 / 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: Primer DNA

MacromoleculeName: Primer DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.339724 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(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: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 297526
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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