[English] 日本語
Yorodumi
- EMDB-5763: Electron cryo-microscopy of two-stranded TubZ filament from B. th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5763
TitleElectron cryo-microscopy of two-stranded TubZ filament from B. thuringiensis
Map dataHelical Reconstruction of two-stranded TubZ-Bt bound to GTPgammaS
Sample
  • Sample: N-terminally tagged full length TubZ from pBtoxis in Bacillus thuringiensis
  • Protein or peptide: ftsZ/tubulin-related protein
Keywordsplasmid segregation / tubulin family / bacterial cytoskeleton
Function / homology
Function and homology information


plasmid partitioning / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Tubulin/FtsZ-like protein TubZ-like, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin-like protein TubZ
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 10.8 Å
AuthorsMontabana EA / Agard DA
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Bacterial tubulin TubZ-Bt transitions between a two-stranded intermediate and a four-stranded filament upon GTP hydrolysis.
Authors: Elizabeth A Montabana / David A Agard /
Abstract: Cytoskeletal filaments form diverse superstructures that are highly adapted for specific functions. The recently discovered TubZ subfamily of tubulins is involved in type III plasmid partitioning ...Cytoskeletal filaments form diverse superstructures that are highly adapted for specific functions. The recently discovered TubZ subfamily of tubulins is involved in type III plasmid partitioning systems, facilitating faithful segregation of low copy-number plasmids during bacterial cell division. One such protein, TubZ-Bt, is found on the large pBtoxis plasmid in Bacillus thuringiensis, and interacts via its extended C terminus with a DNA adaptor protein TubR. Here, we use cryo-electron microscopy to determine the structure of TubZ-Bt filaments and light scattering to explore their mechanism of polymerization. Surprisingly, we find that the helical filament architecture is remarkably sensitive to nucleotide state, changing from two-stranded to four-stranded depending on the ability of TubZ-Bt to hydrolyze GTP. We present pseudoatomic models of both the two- and four-protofilament forms based on cryo-electron microscopy reconstructions (10.8 Å and 6.9 Å, respectively) of filaments formed under different nucleotide states. These data lead to a model in which the two-stranded filament is a necessary intermediate along the pathway to formation of the four-stranded filament. Such nucleotide-directed structural polymorphism is to our knowledge an unprecedented mechanism for the formation of polar filaments.
History
DepositionOct 3, 2013-
Header (metadata) releaseOct 23, 2013-
Map releaseFeb 19, 2014-
UpdateMar 19, 2014-
Current statusMar 19, 2014Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j4t
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j4t
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j4t
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5763.jpg

Downloads & links

-
Map

FileDownload / File: emd_5763.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical Reconstruction of two-stranded TubZ-Bt bound to GTPgammaS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 220 pix.
= 264.66 Å		1.2 Å/pix.
x 220 pix.
= 264.66 Å		1.2 Å/pix.
x 220 pix.
= 264.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.203 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.16868486 - 0.18463798
Average (Standard dev.)-0.00040263 (±0.01309839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-110-110-110
Dimensions220220220
Spacing220220220
CellA=B=C: 264.66 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2031.2031.203
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z264.660264.660264.660
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-110-110-110
NC/NR/NS220220220
D min/max/mean-0.1690.185-0.000

-
Supplemental data

-
Sample components

-
Entire : N-terminally tagged full length TubZ from pBtoxis in Bacillus thu...

EntireName: N-terminally tagged full length TubZ from pBtoxis in Bacillus thuringiensis
Components
  • Sample: N-terminally tagged full length TubZ from pBtoxis in Bacillus thuringiensis
  • Protein or peptide: ftsZ/tubulin-related protein

-
Supramolecule #1000: N-terminally tagged full length TubZ from pBtoxis in Bacillus thu...

SupramoleculeName: N-terminally tagged full length TubZ from pBtoxis in Bacillus thuringiensis
type: sample / ID: 1000
Oligomeric state: Helical filament with two protofilament strands
Number unique components: 1

-
Macromolecule #1: ftsZ/tubulin-related protein

MacromoleculeName: ftsZ/tubulin-related protein / type: protein_or_peptide / ID: 1 / Name.synonym: TubZ-Bt, TubZ / Oligomeric state: helical two-stranded filament / Recombinant expression: Yes
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: serovar israelensis
Molecular weightExperimental: 54.3729 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Tubulin-like protein TubZ / InterPro: Tubulin/FtsZ, GTPase domain

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.7
Details: 100 mM potassium acetate, 5 mM magnesium acetate, 50 mM HEPES
GridDetails: 400 mesh copper grid with holey carbon support, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III
Timed resolved state: TubZ was preheated at 37 degrees and polymerization was initiated with saturating GTPgammaS. TubZ was then incubated for 30 seconds at room temperature before sample application and plunge-freezing.
Method: Blot 4.5 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Astigmatism corrected at 250,000 times magnification
DateMay 26, 2010
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 348 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

DetailsThe particles were aligned using IHRSR. The azimuthal angle refined to 191.84151 degrees and the rise to 22.04811 Angstroms with a right-handed helix.
Final reconstructionApplied symmetry - Helical parameters - Δz: 22.04811 Å
Applied symmetry - Helical parameters - Δ&Phi: 168.15849 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Spider
Details: Final map has been low-pass filtered to 11 Angstrom and high-pass filtered to 35 Angstrom. A B-factor of -452 Angstroms was applied using the program bfactor. A cylindrical mask of radius ...Details: Final map has been low-pass filtered to 11 Angstrom and high-pass filtered to 35 Angstrom. A B-factor of -452 Angstroms was applied using the program bfactor. A cylindrical mask of radius ~78 Angstrom has been applied.
CTF correctionDetails: Whole micrograph

-
Atomic model buiding 1

Initial modelPDB ID:

2xka


Chain - Chain ID: F
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3j4t:
Helical model of TubZ-Bt two-stranded filament

+
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