[English] 日本語
Yorodumi
- EMDB-13672: Sub-tomogram average of Ca. M.lanthanidiphila S-layer obtained fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13672
TitleSub-tomogram average of Ca. M.lanthanidiphila S-layer obtained from whole cell cryo-tomograms
Map dataSub-tomogram average of the S-layer of Ca. M.lanthanidiphila obtained from whole cell cryo-tomograms
Sample
  • Organelle or cellular component: S-layer of Ca.M.lanthanidiphila
KeywordsS-layer / STRUCTURAL PROTEIN
Biological speciesCandidatus Methylomirabilis lanthanidiphila (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsGambelli L / Mesman R
Funding supportEuropean Union, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)339880European Union
Netherlands Organisation for Scientific Research (NWO)024002002European Union
European Research Council (ERC)669371European Union
Netherlands Organisation for Scientific Research (NWO)192.001European Union
European Research Council (ERC)803894European Union
CitationJournal: Front Microbiol / Year: 2021
Title: The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Bacteria.
Authors: Lavinia Gambelli / Rob Mesman / Wouter Versantvoort / Christoph A Diebolder / Andreas Engel / Wiel Evers / Mike S M Jetten / Martin Pabst / Bertram Daum / Laura van Niftrik /
Abstract: bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual ... bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of a distinctive and intriguing case to study.
History
DepositionOct 4, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 61.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 61.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13672.png

Downloads & links

-
Map

FileDownload / File: emd_13672.map.gz / Format: CCP4 / Size: 313.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of the S-layer of Ca. M.lanthanidiphila obtained from whole cell cryo-tomograms
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.92 Å/pix.
x 89 pix.
= 704.88 Å		7.92 Å/pix.
x 31 pix.
= 245.52 Å		7.92 Å/pix.
x 29 pix.
= 229.68 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: 7.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 61.700000000000003 / Movie #1: 61.7
Minimum - Maximum47.478879999999997 - 70.432130000000001
Average (Standard dev.)60.750492000000001 (±1.519258)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin18170
Dimensions312989
Spacing293189
CellA: 229.68001 Å / B: 245.52 Å / C: 704.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.927.927.92
M x/y/z293189
origin x/y/z0.0000.0000.000
length x/y/z229.680245.520704.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS17180
NC/NR/NS293189
D min/max/mean47.47970.43260.750

-
Supplemental data

-
Sample components

-
Entire : S-layer of Ca.M.lanthanidiphila

EntireName: S-layer of Ca.M.lanthanidiphila
Components
  • Organelle or cellular component: S-layer of Ca.M.lanthanidiphila

-
Supramolecule #1: S-layer of Ca.M.lanthanidiphila

SupramoleculeName: S-layer of Ca.M.lanthanidiphila / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: 3ml Ca. M.lanthanidiphila floculant biomass was dispersed using a ball bearing homogenizer with 8um clearance.
Source (natural)Organism: Candidatus Methylomirabilis lanthanidiphila (bacteria)
Location in cell: on top of outer membrane
Molecular weightTheoretical: 31.6 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 20.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
Details: 2 microlitre sample was mixed with 0.5 microlitre 10 nm ProteinA gold solution Grids were plunge frozen in liquid ethane, blot force 1, blot time 3 sec..
DetailsDispersed cells from floculant biomass

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.68 µm / Calibrated defocus min: 4.13 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 33000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMax: 93.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Average exposure time: 0.3835 sec. / Average electron dose: 1.63 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 3 / Number images used: 6000 / Reference model: averaged from hand picked particles / Method: random grid / Software - Name: PEET (ver. 1.14.0)
Details: Used binnend tomograms. Excized sub-volumes of the S-layer with the slicer tool, applied a grid model and saved the grid model after projection on the whole tomogram.
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: PEET (ver. 1.14.0) / Details: resolution obtained from FFT of obtainded average / Number subtomograms used: 1330

+
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