[English] 日本語
Yorodumi
- PDB-7lmb: Tetrahymena telomerase T5D5 structure at 3.8 Angstrom -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lmb
TitleTetrahymena telomerase T5D5 structure at 3.8 Angstrom
Components
  • (Telomerase holoenzyme ...) x 3
  • Telomerase La-related protein p65
  • Telomerase RNA
  • Telomerase associated protein p50
  • Telomerase reverse transcriptase
  • telomere DNA
KeywordsREPLICATION/RNA/DNA / telomerase / polymerase / reverse transcriptase / ribonucleoprotein / REPLICATION / REPLICATION-RNA-DNA complex
Function / homology
Function and homology information


telomerase catalytic core complex assembly / telomerase RNA stabilization / : / 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 / : / 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 / La protein, xRRM domain / xRRM domain profile. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain ...: / Telomerase reverse transcriptase TEN domain / Replication factor A protein 3 / Replication factor A protein 3 / La protein, xRRM domain / xRRM domain profile. / 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 domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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-associated protein of 50 kDa ...: / 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-associated protein of 50 kDa / Telomerase reverse transcriptase / La-related protein 7 homolog
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHe, Y. / Wang, Y. / Liu, B. / Helmling, C. / Susac, L. / Cheng, R. / Zhou, Z.H. / Feigon, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131901 United States
National Science Foundation (NSF, United States)MCB2016540 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
CitationJournal: Nature / Year: 2021
Title: Structures of telomerase at several steps of telomere repeat synthesis.
Authors: Yao He / Yaqiang Wang / Baocheng Liu / Christina Helmling / Lukas Sušac / Ryan Cheng / Z Hong Zhou / Juli Feigon /
Abstract: Telomerase is unique among the reverse transcriptases in containing a noncoding RNA (known as telomerase RNA (TER)) that includes a short template that is used for the processive synthesis of G-rich ...Telomerase is unique among the reverse transcriptases in containing a noncoding RNA (known as telomerase RNA (TER)) that includes a short template that is used for the processive synthesis of G-rich telomeric DNA repeats at the 3' ends of most eukaryotic chromosomes. Telomerase maintains genomic integrity, and its activity or dysregulation are critical determinants of human longevity, stem cell renewal and cancer progression. Previous cryo-electron microscopy structures have established the general architecture, protein components and stoichiometries of Tetrahymena and human telomerase, but our understandings of the details of DNA-protein and RNA-protein interactions and of the mechanisms and recruitment involved remain limited. Here we report cryo-electron microscopy structures of active Tetrahymena telomerase with telomeric DNA at different steps of nucleotide addition. Interactions between telomerase reverse transcriptase (TERT), TER and DNA reveal the structural basis of the determination of the 5' and 3' template boundaries, handling of the template-DNA duplex and separation of the product strand during nucleotide addition. The structure and binding interface between TERT and telomerase protein p50 (a homologue of human TPP1) define conserved interactions that are required for telomerase activation and recruitment to telomeres. Telomerase La-related protein p65 remodels several regions of TER, bridging the 5' and 3' ends and the conserved pseudoknot to facilitate assembly of the TERT-TER catalytic core.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-23439
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Telomerase RNA
C: telomere DNA
H: Telomerase La-related protein p65
A: Telomerase reverse transcriptase
D: Telomerase holoenzyme Teb1 subunit
E: Telomerase holoenzyme Teb2 subunit
F: Telomerase holoenzyme Teb3 subunit
G: Telomerase associated protein p50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,2669
Polymers432,2008
Non-polymers651
Water00
1


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

-
Components

-
Protein , 3 types, 3 molecules HAG

#3: Protein Telomerase La-related protein p65 / Telomerase-associated protein of 65 kDa / p65


Mass: 64207.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: W7X6T2
#4: 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 p50 / p50


Mass: 50049.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: D2CVN8

-
Telomerase holoenzyme ... , 3 types, 3 molecules DEF

#5: Protein Telomerase holoenzyme Teb1 subunit / Telomerase-associated protein of 82 kDa / p82


Mass: 82040.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: D2CVN6
#6: 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
#7: Protein Telomerase holoenzyme 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

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

#1: RNA chain Telomerase RNA


Mass: 50746.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: GenBank: 15148878
#2: DNA chain telomere DNA


Mass: 6668.261 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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Tetrahymena telomerase T5D5 structure / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 FIELD
Image recordingElectron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120360 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00419168
ELECTRON MICROSCOPYf_angle_d0.6126576
ELECTRON MICROSCOPYf_dihedral_angle_d19.9333881
ELECTRON MICROSCOPYf_chiral_restr0.0423065
ELECTRON MICROSCOPYf_plane_restr0.0042809

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • 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

-
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

Read more