[English] 日本語
Yorodumi
- EMDB-3247: Subtomogram average of a piliated type IVa pilus machine in wild-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3247
TitleSubtomogram average of a piliated type IVa pilus machine in wild-type Myxococcus xanthus cells
Map dataSubtomogram average of a piliated type IVa pilus machine in wild-type Myxococcus xanthus cells
Sample
  • Sample: Wild-type Myxococcus xanthus DK1622 cells
  • Organelle or cellular component: Type IVa pilus
Keywordstype IV pilus / motor / motility / adhesion
Function / homology
Function and homology information


type IV pilus assembly / type IV pilus-dependent motility / pilus assembly / protein secretion / cell outer membrane / cell division / ATP hydrolysis activity / ATP binding / membrane / metal ion binding ...type IV pilus assembly / type IV pilus-dependent motility / pilus assembly / protein secretion / cell outer membrane / cell division / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Type IV pilus inner membrane component PilN / Fimbrial assembly protein (PilN) / Type IV pilus inner membrane component PilO / : / Pilus assembly protein, PilO / Type IV pilus inner membrane component PilM / Type IV pilus assembly protein PilM; / GspF/PilC family / Type IV pilus inner membrane component PilP / ATPase, type IV, pilus assembly, PilB ...Type IV pilus inner membrane component PilN / Fimbrial assembly protein (PilN) / Type IV pilus inner membrane component PilO / : / Pilus assembly protein, PilO / Type IV pilus inner membrane component PilM / Type IV pilus assembly protein PilM; / GspF/PilC family / Type IV pilus inner membrane component PilP / ATPase, type IV, pilus assembly, PilB / Type II secretion system protein GspF domain / Type II secretion system GspF domain superfamily / Type II secretion system (T2SS), protein F / Pilus assembly protein, PilP / Type IV pilus secretin PilQ / AMIN domain / AMIN domain / SHS2 domain inserted in FtsA / Type II secretion system protein GspE, N-terminal / MshEN domain / Cell division protein FtsA / Type II secretion system protein GspE, N-terminal superfamily / Secretin and TonB N terminus short domain / Bacterial type II secretion system protein E signature. / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Type II/IV secretion system protein / Type II/IV secretion system protein / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Translation elongation factor EF1B/ribosomal protein S6 / ATPase, nucleotide binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type IV pilus assembly ATPase PilB / Type IV pilus assembly protein PilC / Type IV pilus biogenesis protein PilM / LysM domain protein / PilP / PilO / PilN / PilQ
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
Methodsubtomogram averaging / cryo EM
AuthorsChang YW / Rettberg LA / Treuner-Lange A / Iwasa J / Sogaard-Andersen L / Jensen GJ
CitationJournal: Science / Year: 2016
Title: Architecture of the type IVa pilus machine.
Authors: Yi-Wei Chang / Lee A Rettberg / Anke Treuner-Lange / Janet Iwasa / Lotte Søgaard-Andersen / Grant J Jensen /
Abstract: Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of ...Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.
History
DepositionNov 22, 2015-
Header (metadata) releaseJan 27, 2016-
Map releaseMar 23, 2016-
UpdateMar 23, 2016-
Current statusMar 23, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0575
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0575
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3jc8
  • Surface level: 0.0575
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jc8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3247.tif

emd_3247_1.tif

Downloads & links

-
Map

FileDownload / File: emd_3247.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of a piliated type IVa pilus machine in wild-type Myxococcus xanthus cells
Voxel sizeX=Y=Z: 7.8 Å
Density
Contour LevelBy AUTHOR: 0.0575 / Movie #1: 0.0575
Minimum - Maximum-0.08641942 - 0.16059881
Average (Standard dev.)0.01208199 (±0.05333117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-30-60-60
Dimensions1408080
Spacing1408080
CellA: 624.0 Å / B: 1092.0 Å / C: 624.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z8014080
origin x/y/z0.0000.0000.000
length x/y/z624.0001092.000624.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-60-30-60
NC/NR/NS8014080
D min/max/mean-0.0860.1610.012

-
Supplemental data

-
Sample components

-
Entire : Wild-type Myxococcus xanthus DK1622 cells

EntireName: Wild-type Myxococcus xanthus DK1622 cells
Components
  • Sample: Wild-type Myxococcus xanthus DK1622 cells
  • Organelle or cellular component: Type IVa pilus

-
Supramolecule #1000: Wild-type Myxococcus xanthus DK1622 cells

SupramoleculeName: Wild-type Myxococcus xanthus DK1622 cells / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Type IVa pilus

SupramoleculeName: Type IVa pilus / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No
Source (natural)Organism: Myxococcus xanthus (bacteria) / Strain: DK1622

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Instrument: FEI VITROBOT MARK III

-
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 / Nominal magnification: 27500
Specialist opticsEnergy filter - Name: GATAN / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
DateAug 26, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 150 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Software - Name: IMOD, TOMO3D, PEET / Number subtomograms used: 134

+
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