[English] 日本語
Yorodumi
- PDB-5kmz: Solution NMR structure of Tetrahymena telomerase RNA pseudoknot -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kmz
TitleSolution NMR structure of Tetrahymena telomerase RNA pseudoknot
ComponentsTelomerase RNA pseudoknot
KeywordsRNA / telomerase / pseudoknot / triplex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodSOLUTION NMR
AuthorsCash, D.D. / Feigon, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM048123 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007185 United States
National Science Foundation (NSF, United States)MCB1022379 United States
CitationJournal: Science / Year: 2015
Title: Structure of Tetrahymena telomerase reveals previously unknown subunits, functions, and interactions.
Authors: Jiansen Jiang / Henry Chan / Darian D Cash / Edward J Miracco / Rachel R Ogorzalek Loo / Heather E Upton / Duilio Cascio / Reid O'Brien Johnson / Kathleen Collins / Joseph A Loo / Z Hong Zhou / Juli Feigon /
Abstract: Telomerase helps maintain telomeres by processive synthesis of telomere repeat DNA at their 3'-ends, using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). We report the ...Telomerase helps maintain telomeres by processive synthesis of telomere repeat DNA at their 3'-ends, using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). We report the cryo-electron microscopy structure of Tetrahymena telomerase at ~9 angstrom resolution. In addition to seven known holoenzyme proteins, we identify two additional proteins that form a complex (TEB) with single-stranded telomere DNA-binding protein Teb1, paralogous to heterotrimeric replication protein A (RPA). The p75-p45-p19 subcomplex is identified as another RPA-related complex, CST (CTC1-STN1-TEN1). This study reveals the paths of TER in the TERT-TER-p65 catalytic core and single-stranded DNA exit; extensive subunit interactions of the TERT essential N-terminal domain, p50, and TEB; and other subunit identities and structures, including p19 and p45C crystal structures. Our findings provide structural and mechanistic insights into telomerase holoenzyme function.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionOct 12, 2016ID: 2N6Q
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Telomerase RNA pseudoknot


Theoretical massNumber of molelcules
Total (without water)9,8891
Polymers9,8891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5110 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain Telomerase RNA pseudoknot


Mass: 9888.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D imino NOESY
122isotropic12D D2O NOESY
132isotropic12D TOCSY
144isotropic12D (H)CCH-COSY, 3D (H)CCH-TOCSY, 2D filtered/edited NOESY, 2D 1H-13C HSQC, 2D 1H-15N HSQC, jNN-COSY
153isotropic12D (H)CCH-COSY, 3D (H)CCH-TOCSY, 2D filtered/edited NOESY, 2D 1H-13C HSQC, 2D 1H-15N HSQC, jNN-COSY
165isotropic12D-HSQC-TROSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM sodium phosphate, 50 mM potassium chloride, 1 mM RNA (31-MER), 90% H2O/10% D2OUnlabel_H2O90% H2O/10% D2O
solution210 mM sodium phosphate, 50 mM potassium chloride, 1 mM RNA (31-MER), 100% D2OUnlabel_D2O100% D2O
solution310 mM sodium phosphate, 50 mM potassium chloride, 1 mM [U-13C; U-15N]-Ade,Ura RNA (31-MER), 90% H2O/10% D2OAU_label90% H2O/10% D2O
solution410 mM sodium phosphate, 50 mM potassium chloride, 1 mM [U-13C; U-15N]-Gua, Cyt RNA (31-MER), 90% H2O/10% D2OGC_label90% H2O/10% D2O
solution510 mM sodium phosphate, 50 mM potassium chloride, 1 mM [U-13C; U-15N]-Ade, Ura, Cyt, Gua RNA (31-MER), 90% H2O/10% D2OAUGC_label90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance1
50 mMpotassium chloridenatural abundance1
1 mMRNA (31-MER)natural abundance1
10 mMsodium phosphatenatural abundance2
50 mMpotassium chloridenatural abundance2
1 mMRNA (31-MER)natural abundance2
10 mMsodium phosphatenatural abundance3
50 mMpotassium chloridenatural abundance3
1 mMRNA (31-MER)[U-13C; U-15N]-Ade,Ura3
10 mMsodium phosphatenatural abundance4
50 mMpotassium chloridenatural abundance4
1 mMRNA (31-MER)[U-13C; U-15N]-Gua, Cyt4
10 mMsodium phosphatenatural abundance5
50 mMpotassium chloridenatural abundance5
1 mMRNA (31-MER)[U-13C; U-15N]-Ade, Ura, Cyt, Gua5
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 6.3 / Pressure: ambient / Temperature: 283 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.42Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.42Schwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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