[English] 日本語
Yorodumi
- EMDB-51025: Focused map 'CI-M' from the alphaproteobacterial respiratory supe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51025
TitleFocused map 'CI-M' from the alphaproteobacterial respiratory supercomplex CI1-CIII2-CIV2
Map dataThis postprocessed .mrc file has been trimmed to a smaller box size of 375 pixels) from the larger box of 600 pixels (i.e., original map which is obtained from 3D-refinement). This is a focused map.
Sample
  • Complex: Respiratory supercomplex CI1-CIII2-CIV2 from alphaproteobacterium
    • Complex: Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxidoreductase)
    • Complex: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase)
    • Complex: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase)
    • Complex: Transmembrane anchored cytochrome c
KeywordsSupercomplex / multi-subunit membrane protein complex / electron transport chain / native purification / ELECTRON TRANSPORT
Biological speciesParacoccus denitrificans PD1222 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsYaikhomba M / Hirst J / Croll TI / Spikes TE / Agip ANA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 and MC_UU_00028/1 United Kingdom
CitationJournal: To Be Published
Title: Entire structure of ancestral alphaproteobacterial complex I reveals the mechanism to prevent deactivation
Authors: Yaikhomba M / Hirst J / Croll TI / Spikes TE
History
DepositionJul 13, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51025.png

Downloads & links

-
Map

FileDownload / File: emd_51025.map.gz / Format: CCP4 / Size: 201.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis postprocessed .mrc file has been trimmed to a smaller box size of 375 pixels) from the larger box of 600 pixels (i.e., original map which is obtained from 3D-refinement). This is a focused map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 375 pix.
= 393. Å		1.05 Å/pix.
x 375 pix.
= 393. Å		1.05 Å/pix.
x 375 pix.
= 393. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0363
Minimum - Maximum-0.08244706 - 0.15166517
Average (Standard dev.)-0.0005178173 (±0.004476699)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions375375375
Spacing375375375
CellA=B=C: 393.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51025_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_51025_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: One of the 2 half maps obtained from...

Fileemd_51025_half_map_1.map
AnnotationOne of the 2 half maps obtained from the 3D refinement procedure. The pixel size here is the nominal one. This is a focused map, obtained after 3D refinement of the subtracted particles.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: One of the 2 half maps obtained from...

Fileemd_51025_half_map_2.map
AnnotationOne of the 2 half maps obtained from the 3D refinement procedure. The pixel size here is the nominal one. This is a focused map, obtained after 3D refinement of the subtracted particles.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Respiratory supercomplex CI1-CIII2-CIV2 from alphaproteobacterium

EntireName: Respiratory supercomplex CI1-CIII2-CIV2 from alphaproteobacterium
Components
  • Complex: Respiratory supercomplex CI1-CIII2-CIV2 from alphaproteobacterium
    • Complex: Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxidoreductase)
    • Complex: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase)
    • Complex: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase)
    • Complex: Transmembrane anchored cytochrome c

-
Supramolecule #1: Respiratory supercomplex CI1-CIII2-CIV2 from alphaproteobacterium

SupramoleculeName: Respiratory supercomplex CI1-CIII2-CIV2 from alphaproteobacterium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

-
Supramolecule #2: Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxido...

SupramoleculeName: Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxidoreductase)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#18, #30
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

-
Supramolecule #3: Alphaproteobacterial respiratory complex III (ubiquinone-cytochro...

SupramoleculeName: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase)
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #19-#23
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

-
Supramolecule #4: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase)

SupramoleculeName: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase)
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #24-#27
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

-
Supramolecule #5: Transmembrane anchored cytochrome c

SupramoleculeName: Transmembrane anchored cytochrome c / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #28-#29
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99946
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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