[English] 日本語
Yorodumi
- EMDB-1639: Proteome organization in a genome-reduced bacterium -RNA-polymera... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1639
TitleProteome organization in a genome-reduced bacterium -RNA-polymeraseof Mycoplasma pneumoniae -
Map dataRNA-polymerase from Mycoplasma pneumoniae
Sample
  • Sample: RNA-polymerase of Mycoplasma pneumoniae
  • Protein or peptide: RNA-polymerase
KeywordsRNA-polymerase / Mycoplasma pneumoniae / single particle
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsKuhner S / vanNoort V / Betts MJ / Leo-Macias A / Batisse C / Rode M / Yamada T / Maier T / Bader S / Beltran-Alvarez P ...Kuhner S / vanNoort V / Betts MJ / Leo-Macias A / Batisse C / Rode M / Yamada T / Maier T / Bader S / Beltran-Alvarez P / Castano-Diez D / Chen W-H / Devos D / Guell Cargol M / Norambuena T / Racke I / Rybin V / Schmidt A / Yus E / Aebersold R / Herrmann R / Bottcher B / Frangakis AS / Russell RB / Serrano L / Bork P / Gavin A-C
CitationJournal: Science / Year: 2009
Title: Proteome organization in a genome-reduced bacterium.
Authors: Sebastian Kühner / Vera van Noort / Matthew J Betts / Alejandra Leo-Macias / Claire Batisse / Michaela Rode / Takuji Yamada / Tobias Maier / Samuel Bader / Pedro Beltran-Alvarez / Daniel ...Authors: Sebastian Kühner / Vera van Noort / Matthew J Betts / Alejandra Leo-Macias / Claire Batisse / Michaela Rode / Takuji Yamada / Tobias Maier / Samuel Bader / Pedro Beltran-Alvarez / Daniel Castaño-Diez / Wei-Hua Chen / Damien Devos / Marc Güell / Tomas Norambuena / Ines Racke / Vladimir Rybin / Alexander Schmidt / Eva Yus / Ruedi Aebersold / Richard Herrmann / Bettina Böttcher / Achilleas S Frangakis / Robert B Russell / Luis Serrano / Peer Bork / Anne-Claude Gavin /
Abstract: The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification- ...The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification-mass spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the majority are novel. About a third of the heteromultimeric complexes show higher levels of proteome organization, including assembly into larger, multiprotein complex entities, suggesting sequential steps in biological processes, and extensive sharing of components, implying protein multifunctionality. Incorporation of structural models for 484 proteins, single-particle electron microscopy, and cellular electron tomograms provided supporting structural details for this proteome organization. The data set provides a blueprint of the minimal cellular machinery required for life.
History
DepositionAug 3, 2009-
Header (metadata) releaseJun 11, 2010-
Map releaseJun 11, 2010-
UpdateJun 11, 2010-
Current statusJun 11, 2010Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1639.png

Downloads & links

-
Map

FileDownload / File: emd_1639.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA-polymerase from Mycoplasma pneumoniae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.2 Å/pix.
x 64 pix.
= 332.8 Å		5.2 Å/pix.
x 64 pix.
= 332.8 Å		5.2 Å/pix.
x 64 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum0.0 - 48.7149
Average (Standard dev.)0.205414 (±1.90841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 332.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean0.00048.7150.205

-
Supplemental data

-
Sample components

-
Entire : RNA-polymerase of Mycoplasma pneumoniae

EntireName: RNA-polymerase of Mycoplasma pneumoniae
Components
  • Sample: RNA-polymerase of Mycoplasma pneumoniae
  • Protein or peptide: RNA-polymerase

-
Supramolecule #1000: RNA-polymerase of Mycoplasma pneumoniae

SupramoleculeName: RNA-polymerase of Mycoplasma pneumoniae / type: sample / ID: 1000 / Details: Sample was fixed following the GRAFIX protocol / Number unique components: 1

-
Macromolecule #1: RNA-polymerase

MacromoleculeName: RNA-polymerase / type: protein_or_peptide / ID: 1 / Name.synonym: Polymerase / Recombinant expression: Yes
Source (natural)Organism: Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Recombinant expressionOrganism: Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: 50mM Hepes, 20% glycerol, 0.075% glutaraldehyde, 100mM NaCl, 1.5 mM MgCl2
StainingType: NEGATIVE
Details: Grids were prepared by sandwich negative stain the sample was adsorbed to carbon on mica and floated on 1 % uranyl acetate the carbon was picked up with an uncoated grid then a second piece ...Details: Grids were prepared by sandwich negative stain the sample was adsorbed to carbon on mica and floated on 1 % uranyl acetate the carbon was picked up with an uncoated grid then a second piece of carbon, which was also floated on 1% uranyl acetate, was picked up with the same grid sandwiching the sample between the two layers of carbon
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Alignment procedureLegacy - Astigmatism: Corrected at 200000 times magnification on graininess of carbon
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 14.22 µm / Number real images: 96
Details: Images were recorded on CCD, no scanning sampling step size was adjusted to calibrated image size
Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 27500
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, SPIDER, EMAN
Details: Spider option BP 32F Back Projection - 3D, Sampled, Interpolated in Fourier space
Number images used: 5324

+
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