[English] 日本語
Yorodumi
- EMDB-29916: Subtomogram average of the AnaS GV shell -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29916
TitleSubtomogram average of the AnaS GV shell
Map dataAnaS GV map
Sample
  • Complex: Stripped Gas vesicles
    • Protein or peptide: Gas vesicles protein shellGas vesicle
Biological speciesDolichospermum flos-aquae (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 8.0 Å
AuthorsDutka P / Metskas LA / Hurt RC / Salahshoor H / Wang TY / Malounda D / Lu GJ / Chou TF / Shapiro MG / Jensen JJ
Funding support2 items
OrganizationGrant numberCountry
Other governmentR01-AI127401
Other governmentR01-EB018975
CitationJournal: Structure / Year: 2023
Title: Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET.
Authors: Przemysław Dutka / Lauren Ann Metskas / Robert C Hurt / Hossein Salahshoor / Ting-Yu Wang / Dina Malounda / George J Lu / Tsui-Fen Chou / Mikhail G Shapiro / Grant J Jensen /
Abstract: Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical ...Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a β sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.
History
DepositionFeb 25, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29916.png

Downloads & links

-
Map

FileDownload / File: emd_29916.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnaS GV map
Voxel sizeX=Y=Z: 1.687 Å
Density
Contour LevelBy AUTHOR: 0.722
Minimum - Maximum-0.7100953 - 1.2264725
Average (Standard dev.)0.009426147 (±0.11186054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 283.41602 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_29916_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: AnaS GV map (half2)

Fileemd_29916_half_map_1.map
AnnotationAnaS GV map (half2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: AnaS GV map (half1)

Fileemd_29916_half_map_2.map
AnnotationAnaS GV map (half1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Stripped Gas vesicles

EntireName: Stripped Gas vesicles
Components
  • Complex: Stripped Gas vesicles
    • Protein or peptide: Gas vesicles protein shellGas vesicle

-
Supramolecule #1: Stripped Gas vesicles

SupramoleculeName: Stripped Gas vesicles / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dolichospermum flos-aquae (bacteria)

-
Macromolecule #1: Gas vesicles protein shell

MacromoleculeName: Gas vesicles protein shell / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Dolichospermum flos-aquae (bacteria) / Strain: 1403/13F
SequenceString:
AVEKTNSSSS LAEVIDRILD KGIVIDAWVR VSLVGIELLA IEARIVIASV ETYLKYAEAV GLTQS

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.5 / Details: 10 mM Hepes, pH 7.5
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 23 / Number images used: 28887
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 28887

+
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