[English] 日本語
Yorodumi
- EMDB-10678: in-cell elongating expressome from Mycoplasma pneumoniae with foc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10678
Titlein-cell elongating expressome from Mycoplasma pneumoniae with focused refinement on RNAP
Map datain-cell expressome with improved local RNA polymerase density after focused refinement with a local RNAP-30S mask
Sample
  • Cell: wild-type Mycoplasma pneumoniae M129 cells
Biological speciesMycoplasma pneumoniae M129 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 9.2 Å
AuthorsMahamid J / Xue L
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067 Germany
CitationJournal: Science / Year: 2020
Title: In-cell architecture of an actively transcribing-translating expressome.
Authors: Francis J O'Reilly / Liang Xue / Andrea Graziadei / Ludwig Sinn / Swantje Lenz / Dimitry Tegunov / Cedric Blötz / Neil Singh / Wim J H Hagen / Patrick Cramer / Jörg Stülke / Julia Mahamid ...Authors: Francis J O'Reilly / Liang Xue / Andrea Graziadei / Ludwig Sinn / Swantje Lenz / Dimitry Tegunov / Cedric Blötz / Neil Singh / Wim J H Hagen / Patrick Cramer / Jörg Stülke / Julia Mahamid / Juri Rappsilber /
Abstract: Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the ...Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the genome-reduced human pathogen We combined whole-cell cross-linking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at subnanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA at the interface between a NusG-bound elongating RNAP and the ribosome and propose that it can mediate transcription-translation coupling. Translation inhibition dissociated the expressome, whereas transcription inhibition stalled and rearranged it. Thus, the active expressome architecture requires both translation and transcription elongation within the cell.
History
DepositionFeb 19, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.75
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.75
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10678.png

Downloads & links

-
Map

FileDownload / File: emd_10678.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationin-cell expressome with improved local RNA polymerase density after focused refinement with a local RNAP-30S mask
Voxel sizeX=Y=Z: 3.401 Å
Density
Contour LevelBy AUTHOR: 0.75 / Movie #1: 0.75
Minimum - Maximum-0.9564698 - 3.0397694
Average (Standard dev.)0.014675305 (±0.12871355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 680.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.4013.4013.401
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z680.200680.200680.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.9563.0400.015

-
Supplemental data

-
Mask #1

Fileemd_10678_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_10678_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: in-cell expressome with improved local RNA polymerase density...

Fileemd_10678_half_map_1.map
Annotationin-cell expressome with improved local RNA polymerase density after focused refinement with a local RNAP-30S mask, half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: in-cell expressome with improved local RNA polymerase density...

Fileemd_10678_half_map_2.map
Annotationin-cell expressome with improved local RNA polymerase density after focused refinement with a local RNAP-30S mask, half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : wild-type Mycoplasma pneumoniae M129 cells

EntireName: wild-type Mycoplasma pneumoniae M129 cells
Components
  • Cell: wild-type Mycoplasma pneumoniae M129 cells

-
Supramolecule #1: wild-type Mycoplasma pneumoniae M129 cells

SupramoleculeName: wild-type Mycoplasma pneumoniae M129 cells / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
Details: modified Hayflick medium as described in Halbedel, Hames, and Stulke 2004
GridModel: Quantifoil R2/1 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 45 % / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 352 / Number images used: 73858 / Software - Name: Warp (ver. 1.0.6)
CTF correctionSoftware - Name: Warp (ver. 1.0.6)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7)
Details: Following focused refinement with a local mask on RNAP-30S in RELION, post-processing was performed with the expressome mask provided. The local density for RNAP and 30S was improved.
Number subtomograms used: 2952
FSC plot (resolution estimation)

+
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