[English] 日本語
Yorodumi
- EMDB-100061: Cryo-electron tomogram of Geobacter metallireducens, dataset Geo0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-100061
TitleCryo-electron tomogram of Geobacter metallireducens, dataset Geo02, Position 1_2
Map dataCryo-electron tomogram of Geobacter metallireducens, dataset Geo02, Position 1_2
Sample
  • Cell: Geobacter metallireducens GS-15
Keywordsbenzoyl-CoA reductase class II benzoyl-CoA reductase BCR anaerobic degradation anaerobic aromatic compound degradation benzoyl-CoA aromatic ring reduction Geobacter metallireducens anaerobic metabolism oxidoreductase subtomogram averaging in situ cryo-electron tomography / OXIDOREDUCTASE
Biological speciesGeobacter metallireducens GS-15 (bacteria)
Methodelectron tomography / cryo EM
AuthorsTamborrini D / Pascoa TC / Engel BD / Appel L / Kumar A / Kayastha K / Ermler U / Kettler T / Bohn S / Reif-Trauttmansdorff T ...Tamborrini D / Pascoa TC / Engel BD / Appel L / Kumar A / Kayastha K / Ermler U / Kettler T / Bohn S / Reif-Trauttmansdorff T / Schuller JM / Boll M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)European Union
CitationJournal: To Be Published
Title: Coupling of electron-bifurcation modules powers aromatic ring reduction
Authors: Appel L / Kumar A / Tamborrini D / Pascoa TC / Kayastha K / Ermler U / Kettler T / Bohn S / Reif-Trauttmansdorff T / Engel BD / Schuller JM / Boll M
History
DepositionSep 23, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_100061.png

Downloads & links

-
Map

FileDownload / File: emd_100061.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of Geobacter metallireducens, dataset Geo02, Position 1_2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.64 Å/pix.
x 512 pix.
= 3911.68 Å		7.64 Å/pix.
x 1024 pix.
= 7823.36 Å		7.64 Å/pix.
x 1024 pix.
= 7823.36 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.64 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.56319237 - 0.070516974
Average (Standard dev.)-0.0042609656 (±0.007485101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024512
Spacing10241024512
CellA: 7823.36 Å / B: 7823.36 Å / C: 3911.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Geobacter metallireducens GS-15

EntireName: Geobacter metallireducens GS-15 (bacteria)
Components
  • Cell: Geobacter metallireducens GS-15

-
Supramolecule #1: Geobacter metallireducens GS-15

SupramoleculeName: Geobacter metallireducens GS-15 / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Geobacter metallireducens GS-15 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 6.8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 1200 / Focused ion beam - Temperature: 81 K / Focused ion beam - Initial thickness: 2000 / Focused ion beam - Final thickness: 180
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Thermo Scientific Aquilos 2 Cryo-FIB. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsEER files
Final reconstructionSoftware - Name: Warp (ver. 2.0.0) / Number images used: 57
CTF correctionSoftware - Name: Warp (ver. 2.0.0) / Software - details: post M / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

+
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