[English] 日本語
Yorodumi
- PDB-8omr: Human tRNA guanine transglycosylase (TGT) bound to tRNAAsp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8omr
TitleHuman tRNA guanine transglycosylase (TGT) bound to tRNAAsp
Components
  • Queuine tRNA-ribosyltransferase accessory subunit 2
  • Queuine tRNA-ribosyltransferase catalytic subunit 1
  • tRNAAsp
KeywordsRNA BINDING PROTEIN / RNA modification / transglycosylation / nucleid acid-protein complex / tRNA binding
Function / homology
Function and homology information


tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity ...tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Queuine tRNA-ribosyltransferase accessory subunit QTRTD1 / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
9-DEAZAGUANINE / RNA / RNA (> 10) / Queuine tRNA-ribosyltransferase catalytic subunit 1 / Queuine tRNA-ribosyltransferase accessory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSievers, K. / Neumann, P. / Susac, L. / Trowitzsch, S. / Tampe, R. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Structure / Year: 2024
Title: Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase.
Authors: Katharina Sievers / Piotr Neumann / Lukas Sušac / Stefano Da Vela / Melissa Graewert / Simon Trowitzsch / Dmitri Svergun / Robert Tampé / Ralf Ficner /
Abstract: Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine ...Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase catalytic subunit 1
B: Queuine tRNA-ribosyltransferase accessory subunit 2
C: tRNAAsp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4576
Polymers115,1763
Non-polymers2813
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, assembly was verified by SEC-SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7200 Å2
ΔGint-38 kcal/mol
Surface area43440 Å2
MethodPISA

-
Components

#1: Protein Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 44251.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Zn ion and 9DG are ligands / Source: (gene. exp.) Homo sapiens (human) / Gene: QTRT1, TGT, TGUT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BXR0, tRNA-guanosine34 preQ1 transglycosylase
#2: Protein Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1


Mass: 46775.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Zn is an ion / Source: (gene. exp.) Homo sapiens (human) / Gene: QTRT2, QTRTD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H974
#3: RNA chain tRNAAsp


Mass: 24148.312 Da / Num. of mol.: 1 / Mutation: U1A, C2G, C3G, G69C, G70C, A71U / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-9DG / 9-DEAZAGUANINE


Mass: 150.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 44.46 sec. / Electron dose: 62.1 e/Å2 / Film or detector model: OTHER
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 463140 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037837
ELECTRON MICROSCOPYf_angle_d0.68210955
ELECTRON MICROSCOPYf_dihedral_angle_d11.8671700
ELECTRON MICROSCOPYf_chiral_restr0.0381295
ELECTRON MICROSCOPYf_plane_restr0.0051135

+
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