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- PDB-6d6v: CryoEM structure of Tetrahymena telomerase with telomeric DNA at ... -

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Basic information

Entry
Database: PDB / ID: 6d6v
TitleCryoEM structure of Tetrahymena telomerase with telomeric DNA at 4.8 Angstrom resolution
Components
  • (Telomerase holoenzyme ...) x 2
  • (Telomerase-associated protein ...) x 2
  • DNA (5'-D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3')
  • RNA (159-MER)
  • Telomerase associated protein p65
  • Telomerase reverse transcriptase
KeywordsREPLICATION / Telomerase / telomere
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 / OB-fold nucleic acid binding 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
: / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Replication protein A 32 kDa subunit / Replication protein A 14 kDa subunit / Telomeric repeat-binding subunit 1 / Telomerase reverse transcriptase ...: / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Replication protein A 32 kDa subunit / Replication protein A 14 kDa subunit / Telomeric repeat-binding subunit 1 / Telomerase reverse transcriptase / La-related protein 7 homolog / La-related protein 7 homolog
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsJiang, J. / Wang, Y. / Susac, L. / Chan, H. / Basu, R. / Zhou, Z.H. / Feigon, J.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM048123 United States
National Science Foundation (NSF, United States)MCB1517625 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007185 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
American Heart Association14POST18870059 United States
CitationJournal: Cell / Year: 2018
Title: Structure of Telomerase with Telomeric DNA.
Authors: Jiansen Jiang / Yaqiang Wang / Lukas Sušac / Henry Chan / Ritwika Basu / Z Hong Zhou / Juli Feigon /
Abstract: Telomerase is an RNA-protein complex (RNP) that extends telomeric DNA at the 3' ends of chromosomes using its telomerase reverse transcriptase (TERT) and integral template-containing telomerase RNA ...Telomerase is an RNA-protein complex (RNP) that extends telomeric DNA at the 3' ends of chromosomes using its telomerase reverse transcriptase (TERT) and integral template-containing telomerase RNA (TER). Its activity is a critical determinant of human health, affecting aging, cancer, and stem cell renewal. Lack of atomic models of telomerase, particularly one with DNA bound, has limited our mechanistic understanding of telomeric DNA repeat synthesis. We report the 4.8 Å resolution cryoelectron microscopy structure of active Tetrahymena telomerase bound to telomeric DNA. The catalytic core is an intricately interlocked structure of TERT and TER, including a previously structurally uncharacterized TERT domain that interacts with the TEN domain to physically enclose TER and regulate activity. This complete structure of a telomerase catalytic core and its interactions with telomeric DNA from the template to telomere-interacting p50-TEB complex provides unanticipated insights into telomerase assembly and catalytic cycle and a new paradigm for a reverse transcriptase RNP.
History
DepositionApr 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Telomerase reverse transcriptase
D: Telomerase-associated protein 82
F: Telomerase holoenzyme TEB heterotrimer Teb3 subunit
E: Telomerase holoenzyme Teb2 subunit
B: RNA (159-MER)
C: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3')
G: Telomerase-associated protein 50
H: Telomerase associated protein p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,9879
Polymers394,9228
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules AH

#1: Protein Telomerase reverse transcriptase / / Telomerase catalytic subunit / Telomerase subunit P133


Mass: 133486.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: O77448, RNA-directed DNA polymerase
#8: Protein Telomerase associated protein p65


Mass: 64207.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q6JXI6, UniProt: W7X6T2*PLUS

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Telomerase-associated protein ... , 2 types, 2 molecules DG

#2: Protein Telomerase-associated protein 82


Mass: 82040.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: D2CVN6
#7: Protein Telomerase-associated protein 50


Mass: 13379.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)

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Telomerase holoenzyme ... , 2 types, 2 molecules FE

#3: Protein Telomerase holoenzyme TEB heterotrimer Teb3 subunit /


Mass: 14007.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A0A0U8UFF4
#4: Protein Telomerase holoenzyme Teb2 subunit /


Mass: 30993.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A0A0U8TRG9

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RNA chain / DNA chain / Non-polymers , 3 types, 3 molecules BC

#5: RNA chain RNA (159-MER)


Mass: 50746.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: GenBank: 15148878
#6: DNA chain DNA (5'-D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3')


Mass: 6059.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsTHE AUTHORS STATE THAT FOR P50 THEY WERE ONLY ABLE TO TRACE THE PROTEIN BACKBONE IN THE DENSITY ...THE AUTHORS STATE THAT FOR P50 THEY WERE ONLY ABLE TO TRACE THE PROTEIN BACKBONE IN THE DENSITY CORRESPONDING TO 157 RESIDUES, BUT COULD NOT ASSIGN SEQUENCE. ALTHOUGH THE SEQUENCE IS UNAVAILABLE FOR MODELED CHAIN G, THEY ARE CERTAIN THAT CHAIN G CORRESPONDS TO P50 WITH FULL-LENGTH SEQUENCE: MKLLLQNQNIFQKLKNTLNGCIKKFYDTYQDLEQMQKFEMIVEDKLLFRYSCSQSEMFSAQ IQAHYLEKRVLQLTDGNVKYIVNFRDKGVLDKANFFDTPNNSLVIIRQWSYEIYYTKNTFQ INLVIDEMRCIDIITTIFYCKLELDFTQGIKGISKSSSFSNQIYEYSAQYYKAIQLLKKLL INDSYISELYNSTKSKQQPRLFIFQSFKPKMNLAEQNLSRQFEQCQQDDFGDGCLLQIVNY THQSLKQIENKNNSNQIVNGQNEISKKKRVLKSNEDLYKISLQKQLKIFQEEEIELHSQST IRNQTNQQLETFESDTSKRNSEKILHSINELNTSKQKVNQMNSSQHQIQKLENNNLNKNIL NQINENDIKNELEERQQQHLTQSFNSKAQLKKIITLKKNQDILLFKPQEQEGSKKY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Endogenous assembled Tetrahymena telomerase bound with telomeric DNA
Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 12 sec. / Electron dose: 52 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
4CTFFINDCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52506 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01317205
ELECTRON MICROSCOPYf_angle_d1.69124054
ELECTRON MICROSCOPYf_dihedral_angle_d15.5039991
ELECTRON MICROSCOPYf_chiral_restr0.0842813
ELECTRON MICROSCOPYf_plane_restr0.012442

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