[English] 日本語
Yorodumi
- PDB-6rib: Cryo-EM reconstruction of Thermus thermophilus bactofilin double ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rib
TitleCryo-EM reconstruction of Thermus thermophilus bactofilin double helical filaments
Componentsbactofilin
KeywordsPROTEIN FIBRIL / Prokaryotic cytoskeletons
Function / homologyBactofilin A/B / Polymer-forming cytoskeletal / Polymer-forming cytoskeletal protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDeng, X. / Lowe, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)U105184326 United Kingdom
CitationJournal: Nat Microbiol / Year: 2019
Title: The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity.
Authors: Xian Deng / Andres Gonzalez Llamazares / James M Wagstaff / Victoria L Hale / Giuseppe Cannone / Stephen H McLaughlin / Danguole Kureisaite-Ciziene / Jan Löwe /
Abstract: Bactofilins are small β-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions, from cell stalk formation in Caulobacter crescentus to ...Bactofilins are small β-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions, from cell stalk formation in Caulobacter crescentus to chromosome segregation and motility in Myxococcus xanthus. However, the precise molecular architecture of bactofilin filaments has remained unclear. Here, sequence analysis and electron microscopy results reveal that, in addition to being widely distributed across bacteria and archaea, bactofilins are also present in a few eukaryotic lineages such as the Oomycetes. Electron cryomicroscopy analysis demonstrated that the sole bactofilin from Thermus thermophilus (TtBac) forms constitutive filaments that polymerize through end-to-end association of the β-helical domains. Using a nanobody, we determined the near-atomic filament structure, showing that the filaments are non-polar. A polymerization-impairing mutation enabled crystallization and structure determination, while reaffirming the lack of polarity and the strength of the β-stacking interface. To confirm the generality of the lack of polarity, we performed coevolutionary analysis on a large set of sequences. Finally, we determined that the widely conserved N-terminal disordered tail of TtBac is responsible for direct binding to lipid membranes, both on liposomes and in Escherichia coli cells. Membrane binding is probably a common feature of these widespread but only recently discovered filaments of the prokaryotic cytoskeleton.
History
DepositionApr 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4887
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4887
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: bactofilin
B: bactofilin
C: bactofilin
D: bactofilin
E: bactofilin
F: bactofilin
G: bactofilin
H: bactofilin
I: bactofilin
J: bactofilin
K: bactofilin
L: bactofilin
M: bactofilin
N: bactofilin
O: bactofilin
P: bactofilin
Q: bactofilin
R: bactofilin
S: bactofilin
T: bactofilin
U: bactofilin
V: bactofilin


Theoretical massNumber of molelcules
Total (without water)289,12622
Polymers289,12622
Non-polymers00
Water00
1
A: bactofilin
C: bactofilin
D: bactofilin
G: bactofilin
H: bactofilin
K: bactofilin
L: bactofilin
O: bactofilin
P: bactofilin
S: bactofilin
T: bactofilin


Theoretical massNumber of molelcules
Total (without water)144,56311
Polymers144,56311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
B: bactofilin
E: bactofilin
F: bactofilin
I: bactofilin
J: bactofilin
M: bactofilin
N: bactofilin
Q: bactofilin
R: bactofilin
U: bactofilin
V: bactofilin


Theoretical massNumber of molelcules
Total (without water)144,56311
Polymers144,56311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
bactofilin


Mass: 13142.075 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: TTHA1769 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHG1

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: bactofilin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 11
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2130

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 4.89 ° / Axial rise/subunit: 57.46 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 346000 / Details: FSC: map versus refined atomic model / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL

+
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