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- EMDB-14198: Refined, unsharpened map of human telomerase-DNA-TPP1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14198
TitleRefined, unsharpened map of human telomerase-DNA-TPP1 complex
Map dataRefined, unsharpened map of human telomerase-TPP1-DNA
Sample
  • Complex: Complex of telomeric DNA-bound human telomerase with TPP1
    • Protein or peptide: Telomerase reverse transcriptase
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: TPP1
    • RNA: human telomerase RNA
    • DNA: Telomeric DNA
KeywordsReverse transcriptase / ribonucleoprotein / telomerase / telomere / DNA BINDING PROTEIN
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 / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex ...: / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / telomerase activity / shelterin complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / nuclear telomere cap complex / siRNA processing / telomere capping / telomere maintenance via recombination / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / DNA biosynthetic process / RNA-templated transcription / telomeric DNA binding / positive regulation of stem cell proliferation / mitochondrial nucleoid / negative regulation of cellular senescence / replicative senescence / Telomere Extension By Telomerase / 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 / positive regulation of protein binding / response to cadmium ion / telomere maintenance via telomerase / negative regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / positive regulation of D-glucose import / mitochondrion organization / Formation of the beta-catenin:TCF transactivating complex / PML body / regulation of protein stability / positive regulation of miRNA transcription / RNA-directed DNA polymerase / 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 / 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 H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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
Adrenocortical dysplasia homolog (Mouse), isoform CRA_a / Histone H2A / Histone H2B / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSekne Z / Ghanim GE / van Roon AMM / Nguyen THD
Funding support United Kingdom, United States, 2 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/19 United Kingdom
Jane Coffin Childs Postdoctoral Fellowship United States
CitationJournal: Science / Year: 2022
Title: Structural basis of human telomerase recruitment by TPP1-POT1.
Authors: Zala Sekne / George E Ghanim / Anne-Marie M van Roon / Thi Hoang Duong Nguyen /
Abstract: Telomerase maintains genome stability by extending the 3' telomeric repeats at eukaryotic chromosome ends, thereby counterbalancing progressive loss caused by incomplete genome replication. In ...Telomerase maintains genome stability by extending the 3' telomeric repeats at eukaryotic chromosome ends, thereby counterbalancing progressive loss caused by incomplete genome replication. In mammals, telomerase recruitment to telomeres is mediated by TPP1, which assembles as a heterodimer with POT1. We report structures of DNA-bound telomerase in complex with TPP1 and with TPP1-POT1 at 3.2- and 3.9-angstrom resolution, respectively. Our structures define interactions between telomerase and TPP1-POT1 that are crucial for telomerase recruitment to telomeres. The presence of TPP1-POT1 stabilizes the DNA, revealing an unexpected path by which DNA exits the telomerase active site and a DNA anchor site on telomerase that is important for telomerase processivity. Our findings rationalize extensive prior genetic and biochemical findings and provide a framework for future mechanistic work on telomerase regulation.
History
DepositionJan 26, 2022-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_14198.png

Downloads & links

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Map

FileDownload / File: emd_14198.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined, unsharpened map of human telomerase-TPP1-DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 280 pix.
= 305.2 Å		1.09 Å/pix.
x 280 pix.
= 305.2 Å		1.09 Å/pix.
x 280 pix.
= 305.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.030424645 - 0.066774726
Average (Standard dev.)0.00014518636 (±0.0020784985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 305.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z305.200305.200305.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0300.0670.000

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Supplemental data

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Sample components

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Entire : Complex of telomeric DNA-bound human telomerase with TPP1

EntireName: Complex of telomeric DNA-bound human telomerase with TPP1
Components
  • Complex: Complex of telomeric DNA-bound human telomerase with TPP1
    • Protein or peptide: Telomerase reverse transcriptase
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: TPP1
    • RNA: human telomerase RNA
    • DNA: Telomeric DNA

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Supramolecule #1: Complex of telomeric DNA-bound human telomerase with TPP1

SupramoleculeName: Complex of telomeric DNA-bound human telomerase with TPP1
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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPRAPRCRAV RSLLRSHYRE VLPLATFVRR LGPQGWRLVQ RGDP AAFRA LVAQCLVCVP WDARPPPAAP SFRQVSCLKE LVARVLQRLC ERGAKNVLAF GFA LLDGAR GGPPEAFTTS VRSYLPNTVT DALRGSGAWG LLLRRVGDDV LVHLLARCAL FV LVAPSCA ...String:
MPRAPRCRAV RSLLRSHYRE VLPLATFVRR LGPQGWRLVQ RGDP AAFRA LVAQCLVCVP WDARPPPAAP SFRQVSCLKE LVARVLQRLC ERGAKNVLAF GFA LLDGAR GGPPEAFTTS VRSYLPNTVT DALRGSGAWG LLLRRVGDDV LVHLLARCAL FV LVAPSCA YQVCGPPLYQ LGAATQARPP PHASGPRRRL GCERAWNHSV REAGVPLGLP A PGARRRGG SASRSLPLPK RPRRGAAPEP ERTPVGQGSW AHPGRTRGPS DRGFCVVSPA RPAEEATSL EGALSGTRHS HPSVGRQHHA GPPSTSRPPR PWDTPCPPVY AETKHFLYS SGDKEQLRPS FLLSSLRPSL TGARRLVETI FLGSRPWMPG TPRRLPRLPQ RYWQMRPL F LELLGNHAQC PYGVLLKTHC PLRAAVTPAA GVCAREKPQG SVAAPEEEDT DPRRLVQ LL RQHSSPWQVY GFVRACLRRL VPPGLWGSRH NERRFLRNTK KFISLGKHAK LSLQEL TWK MSVRDCAWLR RSPGVGCVPA AEHRLREEIL AKFLHWLMSV YVVELLRSFF YVTET TFQK NRLFFYRKSV WSKLQSIGIR QHLKRVQLRE LSEAEVRQHR EARPALLTSR LRFI PKPDG LRPIVNMDYV VGARTFRREK RAERLTSRVK ALFSVLNYER ARRPGLLGAS VLG LDDIHR AWRTFVLRVR AQDPPPELYF VKVDVTGAYD TIPQDRLTEV IASIIKPQNT YC VRRYAVV QKAAHGHVRK AFKSHVSTLT DLQPYMRQFV AHLQETSPLR DAVVIEQSSS L NEASSGLF DVFLRFMCHH AVRIRGKSYV QCQGIPQGSI LSTLLCSLCY GDMENKLFAG IRRDGLLLR LVDDFLLVTP HLTHAKTFLR TLVRGVPEYG CVVNLRKTVV NFPVEDEAL GGTAFVQMPA HGLFPWCGLL LDTRTLEVQS DYSSYARTSI RASLTFNRGF KAGRNMRR K LFGVLRLKCH SLFLDLQVNS LQTVCTNIYK ILLLQAYRFH ACVLQLPFHQ QVWKNPT FF LRVISDTASL CYSILKAKNA GMSLGAKGAA GPLPSEAVQW LCHQAFLLKL TRHRVT YVP LLGSLRTAQT QLSRKLPGTT LTALEAAANP ALPSDFKTIL D

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Macromolecule #2: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: Kidney
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VRRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGN AARDNKKTRI IPRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK K TESHHKAK GK

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Macromolecule #3: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: Kidney
SequenceString:
MPDPAKSAPA PKKGSKKAVT KVQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVND IFERIAGEAS RLAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV T KYTSSNPR NLSPTKPGGS EDRQPPPSQL SAIPPFCLVL RAGIAGQV

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Macromolecule #4: TPP1

MacromoleculeName: TPP1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRC LVTREALDTS DWEEKEFGFR GTEGRLLLLQ DCGVHVQVAE GGAPAEFYLQ V DRFSLLPT EQPRLRVPGC NQDLDVQKKL YDCLEEHLSE STSSNAGLSL ...String:
MAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRC LVTREALDTS DWEEKEFGFR GTEGRLLLLQ DCGVHVQVAE GGAPAEFYLQ V DRFSLLPT EQPRLRVPGC NQDLDVQKKL YDCLEEHLSE STSSNAGLSL SQLLDEMRED QE HQGALVC LAESCLTLEG PCTAPPVTHW AASRCKATGE AVYTVPSSML CISENDQLIL SSL GPCQRT QGPELPPPDP ALQDLSLTLI ASPPSSPSSS GTPALPGHMS SEESGTSISL LPAL SLAAP DPGQRSSSQP SPAICSAPAT LTPRSPHASR TPSSPLQSCT PSLSPRSHVP SPHQA LVTR PQKPSLEFKE FVGLPCKNRP PFPRTGATRG AQEPCSVWEP PKRHRDGSAF QYEYEP PCT SLCARVQAVR LPPQLMAWAL HFLMDAQPGS EPTPM

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Macromolecule #5: human telomerase RNA

MacromoleculeName: human telomerase RNA / type: rna / ID: 5
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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Macromolecule #6: Telomeric DNA

MacromoleculeName: Telomeric DNA / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG

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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
10.0 %C3H8O3glycerol
2.0 mMMgCl2magnesium chloride
0.05 %IGEPAL 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: 15 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
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 3 / Number real images: 50775 / Average exposure time: 3.0 sec. / Average electron dose: 48.0 e/Å2
Details: Images were collected in movie-mode and fractionated into 48 movie frames
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: 3.0 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

Particle selectionNumber selected: 18744992
Startup modelType of model: EMDB MAP
EMDB ID:

12174

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 144043
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: RELION (ver. 4)

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Atomic model buiding 1

Initial modelPDB ID:

7bg9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL

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