[English] 日本語
Yorodumi
- EMDB-1757: The Structure of TubZ filaments -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1757
TitleThe Structure of TubZ filaments
Map dataDouble helical filaments of TubZ (pBT156) (Uniprot Q8KNP3) from Bacillus thuringiensis serovar israelensis (ATCC 35646) - negatively stained
Sample
  • Sample: Full length TubZ
  • Protein or peptide: Cytomotive filament
KeywordsCytoskeletal / DNA segregation / FtsZ / FtsZ-like / pBtoxis / pBT156 / plasmid partitioning / RepX / tubulin / tubulin-like / TubZ
Biological speciesBacillus thuringiensis (bacteria)
Methodhelical reconstruction / negative staining / Resolution: 35.0 Å
AuthorsAylett CHS / Amos LA / Lowe J
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Filament structure of bacterial tubulin homologue TubZ.
Authors: Christopher H S Aylett / Qing Wang / Katharine A Michie / Linda A Amos / Jan Löwe /
Abstract: Low copy number plasmids often depend on accurate partitioning systems for their continued survival. Generally, such systems consist of a centromere-like region of DNA, a DNA-binding adaptor, and a ...Low copy number plasmids often depend on accurate partitioning systems for their continued survival. Generally, such systems consist of a centromere-like region of DNA, a DNA-binding adaptor, and a polymerizing cytomotive filament. Together these components drive newly replicated plasmids to opposite ends of the dividing cell. The Bacillus thuringiensis plasmid pBToxis relies on a filament of the tubulin/FtsZ-like protein TubZ for its segregation. By combining crystallography and electron microscopy, we have determined the structure of this filament. We explain how GTP hydrolysis weakens the subunit-subunit contact and also shed light on the partitioning of the plasmid-adaptor complex. The double helical superstructure of TubZ filaments is unusual for tubulin-like proteins. Filaments of ParM, the actin-like partitioning protein, are also double helical. We suggest that convergent evolution shapes these different types of cytomotive filaments toward a general mechanism for plasmid separation.
History
DepositionJul 9, 2010-
Header (metadata) releaseJul 23, 2010-
Map releaseOct 29, 2010-
UpdateApr 20, 2016-
Current statusApr 20, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1757.png

Downloads & links

-
Map

FileDownload / File: emd_1757.map.gz / Format: CCP4 / Size: 666 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDouble helical filaments of TubZ (pBT156) (Uniprot Q8KNP3) from Bacillus thuringiensis serovar israelensis (ATCC 35646) - negatively stained
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
4 Å/pix.
x 86 pix.
= 344. Å		4 Å/pix.
x 45 pix.
= 180. Å		4 Å/pix.
x 45 pix.
= 180. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1.2 / Movie #1: 50
Minimum - Maximum-1476.779999999999973 - 1604.220000000000027
Average (Standard dev.)-705.823999999999955 (±844.833999999999946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions454586
Spacing454586
CellA: 180 Å / B: 180 Å / C: 344 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z454586
origin x/y/z0.0000.0000.000
length x/y/z180.000180.000344.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS454586
D min/max/mean-1476.7761604.220-705.824

-
Supplemental data

-
Sample components

-
Entire : Full length TubZ

EntireName: Full length TubZ
Components
  • Sample: Full length TubZ
  • Protein or peptide: Cytomotive filament

-
Supramolecule #1000: Full length TubZ

SupramoleculeName: Full length TubZ / type: sample / ID: 1000 / Details: Negatively stained / Oligomeric state: Double filament / Number unique components: 1

-
Macromolecule #1: Cytomotive filament

MacromoleculeName: Cytomotive filament / type: protein_or_peptide / ID: 1 / Name.synonym: Cytomotive filament / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: Serovar israelensis / Location in cell: Cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28a

-
Experimental details

-
Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 50 mM NaHEPES 7.5 150 mM KCl 5 mM MgCl2 1 mM GTPyS
StainingType: NEGATIVE / Details: 1% Uranyl Acetate
GridDetails: CuRh 300 mesh
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 69000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
TemperatureAverage: 293 K
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: OTHER / Software - Name: MRC
Details: Final maps were calculated from five averaged datasets

+
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