[English] 日本語
Yorodumi
- EMDB-37342: Structural mechanism of inhibition of the Rho transcription termi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37342
TitleStructural mechanism of inhibition of the Rho transcription termination factor by Rof
Map data
Sample
  • Complex: antitermination complex of Rho-Rof
    • Protein or peptide: Rho-Rof complex
KeywordsEscherichia coli Rho-Rof complex / Rho-dependent termination / antitermination / TRANSCRIPTION
Function / homology
Function and homology information


regulation of termination of DNA-templated transcription / ATP-dependent activity, acting on RNA / transcription antitermination / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / RNA binding / ATP binding / membrane ...regulation of termination of DNA-templated transcription / ATP-dependent activity, acting on RNA / transcription antitermination / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / RNA binding / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
Modulator of Rho-dependent transcription termination / Rof-like superfamily / Modulator of Rho-dependent transcription termination (ROF) / Rof/RNase P-like / Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain ...Modulator of Rho-dependent transcription termination / Rof-like superfamily / Modulator of Rho-dependent transcription termination (ROF) / Rof/RNase P-like / Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain / Cold shock protein domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein rof / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhang J / Wang C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270039 China
CitationJournal: Nat Commun / Year: 2024
Title: A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program.
Authors: Jing Zhang / Shuo Zhang / Wei Zhou / Xiang Zhang / Guanjin Li / Ruoxuan Li / Xingyu Lin / Ziying Chen / Fang Liu / Pan Shen / Xiaogen Zhou / Yue Gao / Zhenguo Chen / Yanjie Chao / Chengyuan Wang /
Abstract: Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate ...Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate unwanted premature RNAs and play important roles in bacterial adaptation to changing environments. Although Rho has been discovered for about five decades, the regulation mechanisms of Rho-dependent termination are still not fully elucidated. Here we report that Rof is a conserved antiterminator and determine the cryogenic electron microscopy structure of Rho-Rof antitermination complex. Rof binds to the open-ring Rho hexamer and inhibits the initiation of Rho-dependent termination. Rof's N-terminal α-helix undergoes conformational changes upon binding with Rho, and is key in facilitating Rof-Rho interactions. Rof binds to Rho's primary binding site (PBS) and excludes Rho from binding with PBS ligand RNA at the initiation step. Further in vivo analyses in Salmonella Typhimurium show that Rof is required for virulence gene expression and host cell invasion, unveiling a physiological function of Rof and transcription termination in bacterial pathogenesis.
History
DepositionAug 30, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_37342.png

Downloads & links

-
Map

FileDownload / File: emd_37342.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.19 Å
Density
Contour LevelBy AUTHOR: 0.00451
Minimum - Maximum-0.018273305 - 0.0583769
Average (Standard dev.)0.00006646217 (±0.0016242738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 357.00003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_37342_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37342_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : antitermination complex of Rho-Rof

EntireName: antitermination complex of Rho-Rof
Components
  • Complex: antitermination complex of Rho-Rof
    • Protein or peptide: Rho-Rof complex

-
Supramolecule #1: antitermination complex of Rho-Rof

SupramoleculeName: antitermination complex of Rho-Rof / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

-
Macromolecule #1: Rho-Rof complex

MacromoleculeName: Rho-Rof complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD GFGFLRSAD SSYLAGPDDI YVSPSQIRRF NLRTGDTISG KIRPPKEGER YFALLKVNEV N FDKPENAR NKILFENLTP LHANSRLRME RGNGSTEDLT ARVLDLASPI ...String:
MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD GFGFLRSAD SSYLAGPDDI YVSPSQIRRF NLRTGDTISG KIRPPKEGER YFALLKVNEV N FDKPENAR NKILFENLTP LHANSRLRME RGNGSTEDLT ARVLDLASPI GRGQRGLIVA PP KAGKTML LQNIAQSIAY NHPDCVLMVL LIDERPEEVT EMQRLVKGEV VASTFDEPAS RHV QVAEMV IEKAKRLVEH KKDVIILLDS ITRLARAYNT VVPASGKVLT GGVDANALHR PKRF FGAAR NVEEGGSLTI IATALIDTGS KMDEVIYEEF KGTGNMELHL SRKIAEKRVF PAIDY NRSG TRKEELLTTQ EELQKMWILR KIIHPMGEID AMEFLINKLA MTKTNDDFFE MMKRS MNDT YQPINCDDYD NLELACQHHL MLTLELKDGE KLQAKASDLV SRKNVEYLVV EAAGET REL RLDKITSFSH PEIGTVVVSE S

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1099028

+
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