[English] 日本語
Yorodumi
- EMDB-14340: Cryo-EM structure of Bacillus megaterium gas vesicles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14340
TitleCryo-EM structure of Bacillus megaterium gas vesicles
Map dataMain map, automatically B-factor sharpened with -30 A**2 in cryoSPARC / symmetrized with -3.874 degree rotation, 0.525 A rise
Sample
  • Complex: Helical assembly of GvpB monomers forming the gas vesicle wall
    • Protein or peptide: GvpA2/B from B.megaterium
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHuber ST / Evers W / Jakobi AJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Cell / Year: 2023
Title: Cryo-EM structure of gas vesicles for buoyancy-controlled motility.
Authors: Stefan T Huber / Dion Terwiel / Wiel H Evers / David Maresca / Arjen J Jakobi /
Abstract: Gas vesicles are gas-filled nanocompartments that allow a diverse group of bacteria and archaea to control their buoyancy. The molecular basis of their properties and assembly remains unclear. Here, ...Gas vesicles are gas-filled nanocompartments that allow a diverse group of bacteria and archaea to control their buoyancy. The molecular basis of their properties and assembly remains unclear. Here, we report the 3.2 Å cryo-EM structure of the gas vesicle shell made from the structural protein GvpA that self-assembles into hollow helical cylinders closed off by cone-shaped tips. Two helical half shells connect through a characteristic arrangement of GvpA monomers, suggesting a mechanism of gas vesicle biogenesis. The fold of GvpA features a corrugated wall structure typical for force-bearing thin-walled cylinders. Small pores enable gas molecules to diffuse across the shell, while the exceptionally hydrophobic interior surface effectively repels water. Comparative structural analysis confirms the evolutionary conservation of gas vesicle assemblies and demonstrates molecular features of shell reinforcement by GvpC. Our findings will further research into gas vesicle biology and facilitate molecular engineering of gas vesicles for ultrasound imaging.
#1: Journal: Biorxiv / Year: 2022
Title: Cryo-EM structure of gas vesicles for buoyancy-controlled motility
Authors: Huber ST / Terwiel D / Evers WH / Maresca D / Jakobi AJ
History
DepositionFeb 11, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14340.png

Downloads & links

-
Map

FileDownload / File: emd_14340.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, automatically B-factor sharpened with -30 A**2 in cryoSPARC / symmetrized with -3.874 degree rotation, 0.525 A rise
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 512 pix.
= 701.44 Å		1.37 Å/pix.
x 512 pix.
= 701.44 Å		1.37 Å/pix.
x 512 pix.
= 701.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.985607 - 2.0391986
Average (Standard dev.)0.0094247535 (±0.13545111)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-255-255-255
Dimensions512512512
Spacing512512512
CellA=B=C: 701.44 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14340_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map / symmetrized with -3.874 degree rotation,...

Fileemd_14340_additional_1.map
AnnotationUnsharpened map / symmetrized with -3.874 degree rotation, 0.525 A rise
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_14340_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_14340_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Helical assembly of GvpB monomers forming the gas vesicle wall

EntireName: Helical assembly of GvpB monomers forming the gas vesicle wall
Components
  • Complex: Helical assembly of GvpB monomers forming the gas vesicle wall
    • Protein or peptide: GvpA2/B from B.megaterium

-
Supramolecule #1: Helical assembly of GvpB monomers forming the gas vesicle wall

SupramoleculeName: Helical assembly of GvpB monomers forming the gas vesicle wall
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Molecular weightTheoretical: 9.99 MDa

-
Macromolecule #1: GvpA2/B from B.megaterium

MacromoleculeName: GvpA2/B from B.megaterium / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSIQKSTNSS SLAEVIDRI L DKGIVIDA FA RVSVVGI EIL TIEARV VIAS VDTWL RYAEA VGLL RDDVEE NGL PERSNSS EG QPRFSI

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

Concentration0.45 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-Cltris(hydroxymethyl)aminomethane
50.0 mMNaClSodium chloridesodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA PLUNGER / Details: Blot times between 5 and 11 seconds..
DetailsConcentration measured by OD(500)=3.12 against a sonicated blank.

-
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 / Cs: 2.7 mm / Nominal defocus max: 1.25 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4351 / Average exposure time: 2.4 sec. / Average electron dose: 30.0 e/Å2
Details: One shot per hole 1.37 A/pix 60 fractions over 30 e-/A2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 36295 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: INSILICO MODEL / In silico model: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.3)
Final reconstructionApplied symmetry - Helical parameters - Δz: 0.525 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.874 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 1460
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: 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