[English] 日本語
Yorodumi
- EMDB-2567: Structure of a bacterial Type IV secretion system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2567
TitleStructure of a bacterial Type IV secretion systemSecretion
Map dataStructure of a bacterial Type IV secretion systemSecretion
Sample
  • Sample: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmidSecretion
  • Protein or peptide: Type IV secretion system from R388 conjugative plasmidSecretion
KeywordsType IV secretion system / R388 conjugative plasmid / Escherichia coli / negative stain electron microscopy
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsLow HH / Gubellini F / Rivera-Calzada A / Braun N / Connery S / Dujeancourt A / Lu F / Redzej A / Fronzes R / Orlova EV / Waksman G
CitationJournal: Nature / Year: 2014
Title: Structure of a type IV secretion system.
Authors: Harry H Low / Francesca Gubellini / Angel Rivera-Calzada / Nathalie Braun / Sarah Connery / Annick Dujeancourt / Fang Lu / Adam Redzej / Rémi Fronzes / Elena V Orlova / Gabriel Waksman /
Abstract: Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells, distribute genetic material between bacteria and have shown potential as a tool for the genetic modification ...Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells, distribute genetic material between bacteria and have shown potential as a tool for the genetic modification of human cells. Given the complex choreography of the substrate through the secretion apparatus, the molecular mechanism of the type IV secretion system has proved difficult to dissect in the absence of structural data for the entire machinery. Here we use electron microscopy to reconstruct the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid. We show that eight proteins assemble in an intricate stoichiometric relationship to form an approximately 3 megadalton nanomachine that spans the entire cell envelope. The structure comprises an outer membrane-associated core complex connected by a central stalk to a substantial inner membrane complex that is dominated by a battery of 12 VirB4 ATPase subunits organized as side-by-side hexameric barrels. Our results show a secretion system with markedly different architecture, and consequently mechanism, to other known bacterial secretion systems.
History
DepositionJan 21, 2014-
Header (metadata) releaseFeb 19, 2014-
Map releaseApr 9, 2014-
UpdateApr 23, 2014-
Current statusApr 23, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 43.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 43.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2567.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a bacterial Type IV secretion system
Voxel sizeX=Y=Z: 3.3 Å
Density
Contour LevelBy AUTHOR: 43.5 / Movie #1: 43.5
Minimum - Maximum-1000.0 - 2669.0463867200001
Average (Standard dev.)4.89805698 (±67.904029850000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 633.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.33.33.3
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z633.600633.600633.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-1000.0002669.0464.898

-
Supplemental data

-
Sample components

-
Entire : Structure of a bacterial Type IV secretion system from Escherichi...

EntireName: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmidSecretion
Components
  • Sample: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmidSecretion
  • Protein or peptide: Type IV secretion system from R388 conjugative plasmidSecretion

-
Supramolecule #1000: Structure of a bacterial Type IV secretion system from Escherichi...

SupramoleculeName: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmid
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 3 MDa / Theoretical: 3.4 MDa
Method: Calculation based on stoichiometry determination of individual components within the complex

-
Macromolecule #1: Type IV secretion system from R388 conjugative plasmid

MacromoleculeName: Type IV secretion system from R388 conjugative plasmid
type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: R388 conjugative plasmid
Molecular weightExperimental: 3 MDa / Theoretical: 3.4 MDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pAsk3c

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.01 mg/mL
BufferpH: 8
Details: 50 mM Tris-HCl pH 8.0, 200 mM NaCl, 0.06 % w/v DM-NPG, 0.1 % w/v digitonin, 1 mM DTT and 1mM EDTA
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 2% w/v uranyl acetate for 30 seconds.
GridDetails: Glow-discharged carbon-coated copper grids (Agar Scientific)
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45500
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
DateJun 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 693 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final two d classificationNumber classes: 803
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Number images used: 3200

+
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