[English] 日本語
Yorodumi
- EMDB-15851: Cryo-EM structure of cytochrome bd oxidase from C. glutamicum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15851
TitleCryo-EM structure of cytochrome bd oxidase from C. glutamicum
Map dataRELION masked postprocessing map
Sample
  • Complex: CydAB heterodimer
    • Protein or peptide: Cytochrome bd-type quinol oxidase subunit II
    • Protein or peptide: Cytochrome BD ubiquinol oxidase subunit I
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: HEME B/C
Function / homology
Function and homology information


cytochrome complex / aerobic electron transport chain / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome ubiquinol oxidase subunit 1 / Cytochrome ubiquinol oxidase subunit 2 / Cytochrome bd terminal oxidase subunit I / Cytochrome bd terminal oxidase subunit II
Similarity search - Domain/homology
Cytochrome bd-type quinol oxidase subunit II / Cytochrome BD ubiquinol oxidase subunit I
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsGrund TN / Kusumoto T / Michel H / Sakamoto J / Safarian S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To be published
Title: Cryo-EM structure of cytochrome bd oxidase from C. glutamicum
Authors: Grund TN / Michel H / Safarian S
History
DepositionSep 20, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15851.png

Downloads & links

-
Map

FileDownload / File: emd_15851.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION masked postprocessing map
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.0125
Minimum - Maximum-0.030817082 - 0.058509797
Average (Standard dev.)-5.5398083e-05 (±0.0014957341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.272 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15851_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION masked 3D refinement map

Fileemd_15851_additional_1.map
AnnotationRELION masked 3D refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RELION 3D refinement half map 1

Fileemd_15851_half_map_1.map
AnnotationRELION 3D refinement half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RELION 3D refinement half map 2

Fileemd_15851_half_map_2.map
AnnotationRELION 3D refinement half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CydAB heterodimer

EntireName: CydAB heterodimer
Components
  • Complex: CydAB heterodimer
    • Protein or peptide: Cytochrome bd-type quinol oxidase subunit II
    • Protein or peptide: Cytochrome BD ubiquinol oxidase subunit I
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: HEME B/C

-
Supramolecule #1: CydAB heterodimer

SupramoleculeName: CydAB heterodimer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Molecular weightTheoretical: 93 KDa

-
Macromolecule #1: Cytochrome bd-type quinol oxidase subunit II

MacromoleculeName: Cytochrome bd-type quinol oxidase subunit II / type: protein_or_peptide / ID: 1 / Details: cydB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Molecular weightTheoretical: 36.261582 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum (bacteria)
SequenceString: MDHNTFWFIL IAFLFSGYFL LEGFDFGVGI LAPIIGKDSA ARNTVIRTIG PVWDGNEVWL IVAGGALFAA FPEWYATMFS GMYLPLFLV LVSLIIRVVG LEWRKKVDDP RWQKWSDRAI FIGSWTPPLM WGFIFANILR GMPIKADHTI DAAAALPGMV N VFAILGAL ...String:
MDHNTFWFIL IAFLFSGYFL LEGFDFGVGI LAPIIGKDSA ARNTVIRTIG PVWDGNEVWL IVAGGALFAA FPEWYATMFS GMYLPLFLV LVSLIIRVVG LEWRKKVDDP RWQKWSDRAI FIGSWTPPLM WGFIFANILR GMPIKADHTI DAAAALPGMV N VFAILGAL AFTALFALHG LAFIRLKTAG RVRTDAAKAA PGVALLAAVT GGPFVLWAAI AYGRSWSWIL AVLIIAAVLG GA FALIKDR DGLSFLSTSV AVIGVVALLF SSLFPNVMPT TLADGVSLDI WNASASHYAL TILTWTAAVI APLVVLYQGW TYW VFRKRL HAEPVSA

-
Macromolecule #2: Cytochrome BD ubiquinol oxidase subunit I

MacromoleculeName: Cytochrome BD ubiquinol oxidase subunit I / type: protein_or_peptide / ID: 2 / Details: CydA / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Molecular weightTheoretical: 56.678461 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum (bacteria)
SequenceString: MDVVDIARWQ FGITTVYHFI FVPLTIGLAP LVAIMQTFWQ VTGKEHWYRA TRFFGTVLLI NFAVGVATGI VQEFQFGMNW SEYSRFVGD VFGGPLALEG LIAFFLESVF LGLWIFGWGK IPGWLHTASI WIVAIATNIS AYFIIVANSF MQHPVGAEYN P ETGRAELT ...String:
MDVVDIARWQ FGITTVYHFI FVPLTIGLAP LVAIMQTFWQ VTGKEHWYRA TRFFGTVLLI NFAVGVATGI VQEFQFGMNW SEYSRFVGD VFGGPLALEG LIAFFLESVF LGLWIFGWGK IPGWLHTASI WIVAIATNIS AYFIIVANSF MQHPVGAEYN P ETGRAELT DFWALLTNST ALAAFPHAVA GGFLTAGTFV LGISGWWIIR AHRQAKKAEA EIESKHSMHR PALWVGWWTT VV SSVALFI TGDTQAKLMF VQQPMKMASA ESLCETATDP NFSILTIGTH NNCDTVTHLI DVPFVLPFLA EGKFTGVTLQ GVN QLQAAA EQAYGPGNYS PNLFVTYWSF RAMIGLMLGS LAIAAIAWLL LRKKRTPTGK IARLFQIGSL IAIPFPFLAN SAGW IFTEM GRQPWVVHPN PESAGDARTE MIRMTVDMGV SDHAPWQVWL TLIGFTILYL ILFVVWVWLI RRAVLIGPPE EGAPS VEAK TGPATPIGSD MPMTPLQFTA AAPTTREKE

-
Macromolecule #3: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 3 / Number of copies: 1 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

ChemComp-HDD:
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

-
Macromolecule #4: HEME B/C

MacromoleculeName: HEME B/C / type: ligand / ID: 4 / Number of copies: 2 / Formula: HEB
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEB:
HEME B/C

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 107.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 995398
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
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://pdbjlvh1.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