[English] 日本語
Yorodumi
- EMDB-2183: Structural basis for TetM-mediated tetracycline resistance -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2183
TitleStructural basis for TetM-mediated tetracycline resistance
Map dataCryo EM reconstruction of an E. coli 70S ribosome bound to ribosome protection protein TetM
Sample
  • Sample: Escherichia coli 70S ribosome in complex with ribosome protection protein TetM
  • Complex: Escherichia coli 70S ribosome
  • Protein or peptide: Tetracycline resistance protein TetMTetracycline
Keywordsantibiotics / protein synthesis / resistance / ribosome / TetM / tetracycline / tigecycline / translation
Function / homology
Function and homology information


translation elongation factor activity / translation / response to antibiotic / GTPase activity / GTP binding
Similarity search - Function
Tetracycline resistance protein, C-terminal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site ...Tetracycline resistance protein, C-terminal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tetracycline resistance protein TetM from transposon Tn916 / Tetracycline resistance protein TetM from transposon TnFO1
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Enterococcus faecalis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsDoenhoefer A / Franckenberg S / Wickles S / Berninghausen O / Beckmann R / Wilson DN
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structural basis for TetM-mediated tetracycline resistance.
Authors: Alexandra Dönhöfer / Sibylle Franckenberg / Stephan Wickles / Otto Berninghausen / Roland Beckmann / Daniel N Wilson /
Abstract: Ribosome protection proteins (RPPs) confer tetracycline resistance by binding to the ribosome and chasing the drug from its binding site. The current model for the mechanism of action of RPPs ...Ribosome protection proteins (RPPs) confer tetracycline resistance by binding to the ribosome and chasing the drug from its binding site. The current model for the mechanism of action of RPPs proposes that drug release is indirect and achieved via conformational changes within the drug-binding site induced upon binding of the RPP to the ribosome. Here we report a cryo-EM structure of the RPP TetM in complex with the 70S ribosome at 7.2-Å resolution. The structure reveals the contacts of TetM with the ribosome, including interaction between the conserved and functionally critical C-terminal extension of TetM and the decoding center of the small subunit. Moreover, we observe direct interaction between domain IV of TetM and the tetracycline binding site and identify residues critical for conferring tetracycline resistance. A model is presented whereby TetM directly dislodges tetracycline to confer resistance.
History
DepositionAug 24, 2012-
Header (metadata) releaseSep 5, 2012-
Map releaseOct 10, 2012-
UpdateMay 20, 2015-
Current statusMay 20, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j25
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j25
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j25
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2183.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo EM reconstruction of an E. coli 70S ribosome bound to ribosome protection protein TetM
Voxel sizeX=Y=Z: 1.2374 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.60853577 - 0.69546944
Average (Standard dev.)0.00421186 (±0.0406208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 455.36322 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23739945652171.23739945652171.2373994565217
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z455.363455.363455.363
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S213
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-0.6090.6950.004

-
Supplemental data

-
Sample components

-
Entire : Escherichia coli 70S ribosome in complex with ribosome protection...

EntireName: Escherichia coli 70S ribosome in complex with ribosome protection protein TetM
Components
  • Sample: Escherichia coli 70S ribosome in complex with ribosome protection protein TetM
  • Complex: Escherichia coli 70S ribosome
  • Protein or peptide: Tetracycline resistance protein TetMTetracycline

-
Supramolecule #1000: Escherichia coli 70S ribosome in complex with ribosome protection...

SupramoleculeName: Escherichia coli 70S ribosome in complex with ribosome protection protein TetM
type: sample / ID: 1000 / Number unique components: 2

-
Supramolecule #1: Escherichia coli 70S ribosome

SupramoleculeName: Escherichia coli 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Tetracycline resistance protein TetM

MacromoleculeName: Tetracycline resistance protein TetM / type: protein_or_peptide / ID: 1 / Name.synonym: TetM / Recombinant expression: No
Source (natural)Organism: Enterococcus faecalis (bacteria)
SequenceUniProtKB: Tetracycline resistance protein TetM from transposon Tn916

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8 / Details: 20mM Hepes-KOH pH 7.8, 30 mM NH4Cl and 10 mM MgCl2
GridDetails: Quantifoil grids (3/3) with 2 nm carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV
Method: Blot for 10 seconds before plunging, used 2 layers of filter paper

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: OTHER
DateJul 1, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: Sorting for ribosome conformation and ligand presence was performed
Number images used: 52701

+
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