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- EMDB-14197: Cryo-EM map of human telomerase-DNA-TPP1-POT1 complex (sharpened map) -

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Basic information

Entry
Database: EMDB / ID: EMD-14197
TitleCryo-EM map of human telomerase-DNA-TPP1-POT1 complex (sharpened map)
Map dataPost-process sharpened map of telomerase-DNA-TPP1-POT1
Sample
  • Complex: Complex of telomeric DNA-bound human telomerase with TPP1-POT1
    • Complex: Telomeric DNA
      • DNA: Telomeric DNA
    • Complex: Telomerase reverse transcriptase and telomeric RNA
      • Protein or peptide: Telomerase reverse transcriptase
      • RNA: human telomerase RNA
    • Complex: Histones
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: TPP1-POT1
      • Protein or peptide: Adrenocortical dysplasia homolog (Mouse), isoform CRA_a
      • Protein or peptide: Protection of telomeres protein 1
KeywordsReverse transcriptase / ribonucleoprotein / telomerase / telomere / DNA BINDING PROTEIN / RNA BINDING PROTEIN
Function / homology
Function and homology information


: / positive regulation of DNA strand elongation / G-rich single-stranded DNA binding / telomere assembly / 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 DNA strand elongation / G-rich single-stranded DNA binding / telomere assembly / 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 / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / telomerase catalytic core complex / regulation of double-strand break repair via nonhomologous end joining / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / RNA-templated DNA biosynthetic process / telomerase inhibitor activity / DEAD/H-box RNA helicase binding / establishment of protein localization to telomere / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / single-stranded telomeric DNA binding / siRNA processing / telomere maintenance via recombination / G-rich strand telomeric DNA binding / telomere capping / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / positive regulation of vascular associated smooth muscle cell migration / Removal of the Flap Intermediate from the C-strand / telomerase RNA binding / telomerase holoenzyme complex / : / RNA-templated transcription / DNA biosynthetic process / telomeric DNA binding / positive regulation of stem cell proliferation / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / mitochondrial nucleoid / Telomere Extension By Telomerase / replicative senescence / negative regulation of cellular 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 / response to cadmium ion / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of vascular associated smooth muscle cell proliferation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of telomere maintenance via telomerase / telomere maintenance / Meiotic synapsis / Inhibition of DNA recombination at telomere / positive regulation of nitric-oxide synthase activity / mitochondrion organization / positive regulation of D-glucose import / transcription coactivator binding / Formation of the beta-catenin:TCF transactivating complex / regulation of protein stability / PML body / DNA Damage/Telomere Stress Induced Senescence / positive regulation of miRNA transcription / RNA-directed DNA polymerase / telomerase activity / positive regulation of angiogenesis / structural constituent of chromatin / nucleosome / positive regulation of protein binding / protein-folding chaperone binding / cellular response to hypoxia / negative regulation of neuron apoptotic process / tRNA binding / chromosome, telomeric region / nuclear body / nuclear speck / protein heterodimerization activity / negative regulation of gene expression / RNA-directed RNA polymerase activity / nucleolus / protein homodimerization activity / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane
Similarity search - Function
: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Adrenocortical dysplasia protein / : / Telomerase reverse transcriptase, C-terminal extension / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 ...: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Adrenocortical dysplasia protein / : / Telomerase reverse transcriptase, C-terminal extension / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 / Telomerase ribonucleoprotein complex - RNA binding domain / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / 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 H2A / Histone 2A / 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. / Histone-fold / Nucleic acid-binding, OB-fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Adrenocortical dysplasia homolog (Mouse), isoform CRA_a / Histone H2A / Histone H2B / Telomerase reverse transcriptase / Protection of telomeres protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSekne Z / Ghanim GE
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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing 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
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7qxb
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7qxs
  • Surface level: 0.01
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_14197.png

Downloads & links

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Map

FileDownload / File: emd_14197.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-process sharpened map of telomerase-DNA-TPP1-POT1
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: 0.009 / Movie #1: 0.01
Minimum - Maximum-0.040483523 - 0.07140276
Average (Standard dev.)0.00012686246 (±0.0023267623)
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/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0400.0710.000

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Supplemental data

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Mask #1

Fileemd_14197_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refined half-map 1

Fileemd_14197_half_map_1.map
AnnotationRefined half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refined half-map 2

Fileemd_14197_half_map_2.map
AnnotationRefined half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of telomeric DNA-bound human telomerase with TPP1-POT1

EntireName: Complex of telomeric DNA-bound human telomerase with TPP1-POT1
Components
  • Complex: Complex of telomeric DNA-bound human telomerase with TPP1-POT1
    • Complex: Telomeric DNA
      • DNA: Telomeric DNA
    • Complex: Telomerase reverse transcriptase and telomeric RNA
      • Protein or peptide: Telomerase reverse transcriptase
      • RNA: human telomerase RNA
    • Complex: Histones
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: TPP1-POT1
      • Protein or peptide: Adrenocortical dysplasia homolog (Mouse), isoform CRA_a
      • Protein or peptide: Protection of telomeres protein 1

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Supramolecule #1: Complex of telomeric DNA-bound human telomerase with TPP1-POT1

SupramoleculeName: Complex of telomeric DNA-bound human telomerase with TPP1-POT1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: Telomeric DNA

SupramoleculeName: Telomeric DNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Telomerase reverse transcriptase and telomeric RNA

SupramoleculeName: Telomerase reverse transcriptase and telomeric RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Histones

SupramoleculeName: Histones / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: TPP1-POT1

SupramoleculeName: TPP1-POT1 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6-#7
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
Recombinant expressionOrganism: Homo sapiens (human)
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 #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: Kidney
Molecular weightTheoretical: 14.140584 KDa
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VRRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: Kidney
Molecular weightTheoretical: 18.074932 KDa
SequenceString:
MPDPAKSAPA PKKGSKKAVT KVQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSNPRN LSPTKPGGSE DRQPPPSQLS AIPPFCLVLR A GIAGQV

UniProtKB: Histone H2B

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Macromolecule #6: Adrenocortical dysplasia homolog (Mouse), isoform CRA_a

MacromoleculeName: Adrenocortical dysplasia homolog (Mouse), isoform CRA_a
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.013086 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRCL VTREALDTSD WEEKEFGFR GTEGRLLLLQ DCGVHVQVAE GGAPAEFYLQ VDRFSLLPTE QPRLRVPGCN QDLDVQKKLY DCLEEHLSES T SSNAGLSL ...String:
MAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRCL VTREALDTSD WEEKEFGFR GTEGRLLLLQ DCGVHVQVAE GGAPAEFYLQ VDRFSLLPTE QPRLRVPGCN QDLDVQKKLY DCLEEHLSES T SSNAGLSL SQLLDEMRED QEHQGALVCL AESCLTLEGP CTAPPVTHWA ASRCKATGEA VYTVPSSMLC ISENDQLILS SL GPCQRTQ GPELPPPDPA LQDLSLTLIA SPPSSPSSSG TPALPGHMSS EESGTSISLL PALSLAAPDP GQRSSSQPSP AIC SAPATL TPRSPHASRT PSSPLQSCTP SLSPRSHVPS PHQALVTRPQ KPSLEFKEFV GLPCKNRPPF PRTGATRGAQ EPCS VWEPP KRHRDGSAFQ YEYEPPCTSL CARVQAVRLP PQLMAWALHF LMDAQPGSEP TPM

UniProtKB: Adrenocortical dysplasia homolog (Mouse), isoform CRA_a

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Macromolecule #7: Protection of telomeres protein 1

MacromoleculeName: Protection of telomeres protein 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.520766 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MSLVPATNYI YTPLNQLKGG TIVNVYGVVK FFKPPYLSKG TDYCSVVTIV DQTNVKLTCL LFSGNYEALP IIYKNGDIVR FHRLKIQVY KKETQGITSS GFASLTFEGT LGAPIIPRTS SKYFNFTTED HKMVEALRVW ASTHMSPSWT LLKLCDVQPM Q YFDLTCQL ...String:
MSLVPATNYI YTPLNQLKGG TIVNVYGVVK FFKPPYLSKG TDYCSVVTIV DQTNVKLTCL LFSGNYEALP IIYKNGDIVR FHRLKIQVY KKETQGITSS GFASLTFEGT LGAPIIPRTS SKYFNFTTED HKMVEALRVW ASTHMSPSWT LLKLCDVQPM Q YFDLTCQL LGKAEVDGAS FLLKVWDGTR TPFPSWRVLI QDLVLEGDLS HIHRLQNLTI DILVYDNHVH VARSLKVGSF LR IYSLHTK LQSMNSENQT MLSLEFHLHG GTSYGRGIRV LPESNSDVDQ LKKDLESANL TANQHSDVIC QSEPDDSFPS SGS VSLYEV ERCQQLSATI LTDHQYLERT PLCAILKQKA PQQYRIRAKL RSYKPRRLFQ SVKLHCPKCH LLQEVPHEGD LDII FQDGA TKTPDVKLQN TSLYDSKIWT TKNQKGRKVA VHFVKNNGIL PLSNECLLLI EGGTLSEICK LSNKFNSVIP VRSGH EDLE LLDLSAPFLI QGTIHHYGCK QCSSLRSIQN LNSLVDKTSW IPSSVAEALG IVPLQYVFVM TFTLDDGTGV LEAYLM DSD KFFQIPASEV LMDDDLQKSV DMIMDMFCPP GIKIDAYPWL ECFIKSYNVT NGTDNQICYQ IFDTTVAEDV I

UniProtKB: Protection of telomeres protein 1

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Macromolecule #2: human telomerase RNA

MacromoleculeName: human telomerase RNA / type: rna / ID: 2 / 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: NR_001566.1

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Macromolecule #5: Telomeric DNA

MacromoleculeName: Telomeric DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.501092 KDa
SequenceString:
(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(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: 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: 45871 / 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: 21589656
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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 192871
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)
FSC plot (resolution estimation)

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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
Output model

PDB-7qxb:
Cryo-EM map of human telomerase-DNA-TPP1-POT1 complex (sharpened map)

PDB-7qxs:
Cryo-EM structure of human telomerase-DNA-TPP1-POT1 complex (with POT1 side chains)

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  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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