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- EMDB-31814: masked 5' tail of RNA in biogenesis module of human telomerase ho... -

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Basic information

Entry
Database: EMDB / ID: EMD-31814
Titlemasked 5' tail of RNA in biogenesis module of human telomerase holoenzyme
Map data
Sample
  • Complex: Biogenesis module
    • Protein or peptide: Telomerase Cajal body protein 1
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit DKC1
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 1
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 2
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 3
    • DNA: Telomerase RNA component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsWan F / Ding Y / Yang L / Wu Z / Wu J / Lei M
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-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31814.png

Downloads & links

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Map

FileDownload / File: emd_31814.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: 0.008
Minimum - Maximum-0.02023348 - 0.06638583
Average (Standard dev.)0.00033217092 (±0.0017601186)
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 : Biogenesis module

EntireName: Biogenesis module
Components
  • Complex: Biogenesis module
    • Protein or peptide: Telomerase Cajal body protein 1
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit DKC1
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 1
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 2
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 3
    • DNA: Telomerase RNA component

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Supramolecule #1: Biogenesis module

SupramoleculeName: Biogenesis module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Telomerase Cajal body protein 1

MacromoleculeName: Telomerase Cajal body protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MKTLETQPLA PDCCPSDQDP APAHPSPHAS PMNKNADSEL MPPPPERGDP PRLSPDPVAG SAVSQELREG DPVSLSTPL ETEFGSPSEL SPRIEEQELS ENTSLPAEEA NGSLSEEEAN GPELGSGKAM EDTSGEPAAE D EGDTAWNY SFSQLPRFLS GSWSEFSTQP ...String:
MKTLETQPLA PDCCPSDQDP APAHPSPHAS PMNKNADSEL MPPPPERGDP PRLSPDPVAG SAVSQELREG DPVSLSTPL ETEFGSPSEL SPRIEEQELS ENTSLPAEEA NGSLSEEEAN GPELGSGKAM EDTSGEPAAE D EGDTAWNY SFSQLPRFLS GSWSEFSTQP ENFLKGCKWA PDGSCILTNS ADNILRIYNL PPELYHEGEQ VE YAEMVPV LRMVEGDTIY DYCWYSLMSS AQPDTSYVAS SSRENPIHIW DAFTGELRAS FRAYNHLDEL TAA HSLCFS PDGSQLFCGF NRTVRVFSTA RPGRDCEVRA TFAKKQGQSG IISCIAFSPA QPLYACGSYG RSLG LYAWD DGSPLALLGG HQGGITHLCF HPDGNRFFSG ARKDAELLCW DLRQSGYPLW SLGREVTTNQ RIYFD LDPT GQFLVSGSTS GAVSVWDTDG PGNDGKPEPV LSFLPQKDCT NGVSLHPSLP LLATASGQRV FPEPTE SGD EGEELGLPLL STRHVHLECR LQLWWCGGAP DSSIPDDHQG EKGQGGTEGG VGELI

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Macromolecule #2: H/ACA ribonucleoprotein complex subunit DKC1

MacromoleculeName: H/ACA ribonucleoprotein complex subunit DKC1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MADAEVIILP KKHKKKKERK SLPEEDVAEI QHAEEFLIKP ESKVAKLDTS QWPLLLKNFD KLNVRTTHYT PLACGSNPL KREIGDYIRT GFINLDKPSN PSSHEVVAWI RRILRVEKTG HSGTLDPKVT GCLIVCIERA T RLVKSQQS AGKEYVGIVR LHNAIEGGTQ ...String:
MADAEVIILP KKHKKKKERK SLPEEDVAEI QHAEEFLIKP ESKVAKLDTS QWPLLLKNFD KLNVRTTHYT PLACGSNPL KREIGDYIRT GFINLDKPSN PSSHEVVAWI RRILRVEKTG HSGTLDPKVT GCLIVCIERA T RLVKSQQS AGKEYVGIVR LHNAIEGGTQ LSRALETLTG ALFQRPPLIA AVKRQLRVRT IYESKMIEYD PE RRLGIFW VSCEAGTYIR TLCVHLGLLL GVGGQMQELR RVRSGVMSEK DHMVTMHDVL DAQWLYDNHK DES YLRRVV YPLEKLLTSH KRLVMKDSAV NAICYGAKIM LPGVLRYEDG IEVNQEIVVI TTKGEAICMA IALM TTAVI STCDHGIVAK IKRVIMERDT YPRKWGLGPK ASQKKLMIKQ GLLDKHGKPT DSTPATWKQE YVDYS ESAK KEVVAEVVKA PQVVAEAAKT AKRKRESESE SDETPPAAPQ LIKKEKKKSK KDKKAKAGLE SGAEPG DGD SDTTKKKKKK KKAKEVELVS E

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Macromolecule #3: H/ACA ribonucleoprotein complex subunit 1

MacromoleculeName: H/ACA ribonucleoprotein complex subunit 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSFRGGGRGG FNRGGGGGGF NRGGSSNHFR GGGGGGGGGN FRGGGRGGFG RGGGRGGFNK GQDQGPPERV VLLGEFLHP CEDDIVCKCT TDENKVPYFN APVYLENKEQ IGKVDEIFGQ LRDFYFSVKL SENMKASSFK K LQKFYIDP YKLLPLQRFL PRPPGEKGPP ...String:
MSFRGGGRGG FNRGGGGGGF NRGGSSNHFR GGGGGGGGGN FRGGGRGGFG RGGGRGGFNK GQDQGPPERV VLLGEFLHP CEDDIVCKCT TDENKVPYFN APVYLENKEQ IGKVDEIFGQ LRDFYFSVKL SENMKASSFK K LQKFYIDP YKLLPLQRFL PRPPGEKGPP RGGGRGGRGG GRGGGGRGGG RGGGFRGGRG GGGGGFRGGR GG GFRGRGH

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Macromolecule #4: H/ACA ribonucleoprotein complex subunit 2

MacromoleculeName: H/ACA ribonucleoprotein complex subunit 2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MTKIKADPDG PEAQAEACSG ERTYQELLVN QNPIAQPLAS RRLTRKLYKC IKKAVKQKQI RRGVKEVQKF VNKGEKGIM VLAGDTLPIE VYCHLPVMCE DRNLPYVYIP SKTDLGAAAG SKRPTCVIMV KPHEEYQEAY D ECLEEVQS LPLPL

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Macromolecule #5: H/ACA ribonucleoprotein complex subunit 3

MacromoleculeName: H/ACA ribonucleoprotein complex subunit 3 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MFLQYYLNEQ GDRVYTLKKF DPMGQQTCSA HPARFSPDDK YSRHRITIKK RFKVLMTQQP RPVL

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Macromolecule #6: Telomerase RNA component

MacromoleculeName: Telomerase RNA component / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString: GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGC UUUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU G CCGCCUUC CACCGUUCAU UCUAGAGCAA ...String:
GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGC UUUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU G CCGCCUUC CACCGUUCAU UCUAGAGCAA ACAAAAAAUG UCAGCUGCUG GCCCGUUCGC CCCUCCCGGG GA CCUGCGG CGGGUCGCCU GCCCAGCCCC CGAACCCCGC CUGGAGGCCG CGGUCGGCCC GGGGCUUCUC CGG AGGCAC CCACUGCCAC CGCGAAGAGU UGGGCUCUGU CAGCCGCGGG UCUCUCGGGG GCGAGGGCGA GGUU CAGGC CUUUCAGGCC GCAGGAAGAG GAACGGAGCG AGUCCCCGCG CGCGGCGCGA UUCCCUGAGC UGUGG GACG UGCACCCAGG ACUCGGCUCA CACAUGC

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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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131717
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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