[English] 日本語
Yorodumi
- EMDB-8495: Subtomogram average of the piliated toxin-coregulated pilus machi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8495
TitleSubtomogram average of the piliated toxin-coregulated pilus machine in wild-type Vibrio cholerae cells (aligning IM-parts)
Map dataSubtomogram average of the piliated toxin-coregulated pilus machine in wild-type Vibrio cholerae cells (aligning IM-parts)
Sample
  • Complex: Toxin-coregulated pilus machine
Biological speciesVibrio cholerae (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 50.0 Å
AuthorsChang Y-W / Kjaer A / Jensen GJ
CitationJournal: Nat Microbiol / Year: 2017
Title: Architecture of the Vibrio cholerae toxin-coregulated pilus machine revealed by electron cryotomography.
Authors: Yi-Wei Chang / Andreas Kjær / Davi R Ortega / Gabriela Kovacikova / John A Sutherland / Lee A Rettberg / Ronald K Taylor / Grant J Jensen /
Abstract: Type IV pili (T4P) are filamentous appendages found on many Bacteria and Archaea. They are helical fibres of pilin proteins assembled by a multi-component macromolecular machine we call the basal ...Type IV pili (T4P) are filamentous appendages found on many Bacteria and Archaea. They are helical fibres of pilin proteins assembled by a multi-component macromolecular machine we call the basal body. Based on pilin features, T4P are classified into type IVa pili (T4aP) and type IVb pili (T4bP). T4aP are more widespread and are involved in cell motility, DNA transfer, host predation and electron transfer. T4bP are less prevalent and are mainly found in enteropathogenic bacteria, where they play key roles in host colonization. Following similar work on T4aP machines, here we use electron cryotomography to reveal the three-dimensional in situ structure of a T4bP machine in its piliated and non-piliated states. The specific machine we analyse is the Vibrio cholerae toxin-coregulated pilus machine (TCPM). Although only about half of the components of the TCPM show sequence homology to components of the previously analysed Myxococcus xanthus T4aP machine (T4aPM), we find that their structures are nevertheless remarkably similar. Based on homologies with components of the M. xanthus T4aPM and additional reconstructions of TCPM mutants in which the non-homologous proteins are individually deleted, we propose locations for all eight TCPM components within the complex. Non-homologous proteins in the T4aPM and TCPM are found to form similar structures, suggesting new hypotheses for their functions and evolutionary histories.
History
DepositionDec 1, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseFeb 15, 2017-
UpdateFeb 15, 2017-
Current statusFeb 15, 2017Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 150
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 150
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_8495.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of the piliated toxin-coregulated pilus machine in wild-type Vibrio cholerae cells (aligning IM-parts)
Voxel sizeX=Y=Z: 7.8 Å
Density
Contour LevelBy AUTHOR: 150. / Movie #1: 150
Minimum - Maximum0. - 255.
Average (Standard dev.)118.86309 (±53.859561999999997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1505050
Spacing5015050
CellA: 390.0 Å / B: 1170.0 Å / C: 390.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z5015050
origin x/y/z0.0000.0000.000
length x/y/z390.0001170.000390.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS5015050
D min/max/mean0.000255.000118.863

-
Supplemental data

-
Sample components

-
Entire : Toxin-coregulated pilus machine

EntireName: Toxin-coregulated pilus machine
Components
  • Complex: Toxin-coregulated pilus machine

-
Supramolecule #1: Toxin-coregulated pilus machine

SupramoleculeName: Toxin-coregulated pilus machine / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Vibrio cholerae (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 74 / Number images used: 111 / Software - Name: PEET
CTF correctionSoftware - Name: IMOD
Final 3D classificationSoftware - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET
Final reconstructionResolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: OTHER / Software - Name: Tomo3d / Number subtomograms used: 111

+
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