[English] 日本語
Yorodumi
- EMDB-50520: Cryo-EM structure of the reduced cytochrome bd oxidase from M. tu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50520
TitleCryo-EM structure of the reduced cytochrome bd oxidase from M. tuberculosis
Map data
Sample
  • Complex: Cytochrome BD-I oxidase
    • Protein or peptide: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I)
    • Protein or peptide: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II)
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: MENAQUINONE-9
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: CARDIOLIPIN
  • Ligand: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
KeywordsUbiquinone / Demethylmenaquinone / Cryo-EM / Respiration / Substrate specificity / Disulfide regulation / OXIDOREDUCTASE
Function / homology
Function and homology information


cytochrome complex / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / electron transfer activity / heme binding / 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
Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I) / Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsKayastha K / Bruenle S
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Other government Netherlands
CitationJournal: J Biol Chem / Year: 2025
Title: Menaquinone-specific turnover by Mycobacterium tuberculosis cytochrome bd is redox regulated by the Q-loop disulfide bond.
Authors: Tijn T van der Velden / Kanwal Kayastha / Caspar Y J Waterham / Steffen Brünle / Lars J C Jeuken /
Abstract: Cytochrome bd from Mycobacterium tuberculosis (Mtbd) is a menaquinol oxidase that has gained interest as an antibiotic target because of its importance in survival under infectious conditions. Mtbd ...Cytochrome bd from Mycobacterium tuberculosis (Mtbd) is a menaquinol oxidase that has gained interest as an antibiotic target because of its importance in survival under infectious conditions. Mtbd contains a characteristic disulfide bond that has been hypothesized to allow for Mtbd activity regulation at the enzymatic level, possibly helping M. tuberculosis to rapidly adapt to the hostile environment of the phagosome. Here, the role of the disulfide bond and quinone specificity have been determined by reconstitution of a minimal respiratory chain and the single-particle cryo-EM structure in the disulfide-reduced form. Mtbd was shown to be specific for menaquinone, while regulation by reduction of the Q-loop disulfide bond decreased oxidase activity up to 90%. Structural analysis shows that a salt bridge unique to Mtbd keeps the Q-loop partially structured in its disulfide-reduced form, which could facilitate the rapid activation of Mtbd upon exposure to reactive oxygen species. We signify Mtbd as the first redox sensory terminal oxidase and propose that this helps M. tuberculosis in the defense against reactive oxygen species encountered during infection.
History
DepositionJun 3, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50520.png

Downloads & links

-
Map

FileDownload / File: emd_50520.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0657
Minimum - Maximum-0.22098845 - 0.43607315
Average (Standard dev.)0.0012087795 (±0.012792336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.016 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_50520_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_50520_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_50520_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cytochrome BD-I oxidase

EntireName: Cytochrome BD-I oxidase
Components
  • Complex: Cytochrome BD-I oxidase
    • Protein or peptide: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I)
    • Protein or peptide: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II)
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: MENAQUINONE-9
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: CARDIOLIPIN
  • Ligand: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate

-
Supramolecule #1: Cytochrome BD-I oxidase

SupramoleculeName: Cytochrome BD-I oxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Cytochrome BD-I oxidase bound with Heme B, cis-Heme D, Menaquinone-9, Cardiolipins, PE lipid
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 942 KDa

-
Macromolecule #1: Probable integral membrane cytochrome D ubiquinol oxidase (Subuni...

MacromoleculeName: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I)
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 53.863098 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MNVVDISRWQ FGITTVYHFI FVPLTIGLAP LIAVMQTLWV VTDNPAWYRL TKFFGKLFLI NFAIGVATGI VQEFQFGMNW SEYSRFVGD VFGAPLAMEG LAAFFFESTF IGLWIFGWNR LPRLVHLACI WIVAIAVNVS AFFIIAANSF MQHPVGAHYN P TTGRAELS ...String:
MNVVDISRWQ FGITTVYHFI FVPLTIGLAP LIAVMQTLWV VTDNPAWYRL TKFFGKLFLI NFAIGVATGI VQEFQFGMNW SEYSRFVGD VFGAPLAMEG LAAFFFESTF IGLWIFGWNR LPRLVHLACI WIVAIAVNVS AFFIIAANSF MQHPVGAHYN P TTGRAELS SIVVLLTNNT AQAAFTHTVS GALLTAGTFV AAVSAWWLVR SSTTHADSDT QAMYRPATIL GCWVALAATA GL LFTGDHQ GKLMFQQQPM KMASAESLCD TQTDPNFSVL TVGRQNNCDS LTRVIEVPYV LPFLAEGRIS GVTLQGIRDL QQE YQQRFG PNDYRPNLFV TYWSFRMMIG LMAIPVLFAL IALWLTRGGQ IPNQRWFSWL ALLTMPAPFL ANSAGWVFTE MGRQ PWVVV PNPTGDQLVR LTVKAGVSDH SATVVATSLL MFTLVYAVLA VIWCWLLKRY IVEGPLEHDA EPAAHGAPRD DEVAP LSFA Y

UniProtKB: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I)

-
Macromolecule #2: Probable integral membrane cytochrome D ubiquinol oxidase (Subuni...

MacromoleculeName: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II)
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 37.650957 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MVLQELWFGV IAALFLGFFI LEGFDFGVGM LMAPFAHVGM GDPETHRRTA LNTIGPVWDG NEVWLITAGA AIFAAFPGWY ATVFSALYL PLLAILFGMI LRAVAIEWRG KIDDPKWRTG ADFGIAAGSW LPALLWGVAF AILVRGLPVD ANGHVALSIP D VLNAYTLL ...String:
MVLQELWFGV IAALFLGFFI LEGFDFGVGM LMAPFAHVGM GDPETHRRTA LNTIGPVWDG NEVWLITAGA AIFAAFPGWY ATVFSALYL PLLAILFGMI LRAVAIEWRG KIDDPKWRTG ADFGIAAGSW LPALLWGVAF AILVRGLPVD ANGHVALSIP D VLNAYTLL GGLATAGLFS LYGAVFIALK TSGPIRDDAY RFAVWLSLPV AGLVAGFGLW TQLAYGKDWT WLVLAVAGCA QA AATVLVW RRVSDGWAFM CTLIVVAAVV VLLFGALYPN LVPSTLNPQW SLTIHNASST PYTLKIMTWV TAFFAPLTVA YQT WTYWVF RQRISAERIP PPTGLARRAP

UniProtKB: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II)

-
Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Macromolecule #4: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 4 / Number of copies: 1 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

-
Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 5 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Macromolecule #6: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 6 / Number of copies: 1 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

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

-
Macromolecule #7: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 7 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

-
Macromolecule #8: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

MacromoleculeName: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
type: ligand / ID: 8 / Number of copies: 1 / Formula: CD4
Molecular weightTheoretical: 1.241633 KDa
Chemical component information

ChemComp-CD4:
(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris-Hcl
150.0 mMSodium ChlorideNaCl
0.005 %LMNG

Details: 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 0.005% LMNG
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: OTHER / Details: 15 mAmp
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: Objective aperture of 100 um
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 14078 / Average exposure time: 4.04 sec. / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 15300000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7nkz

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.0) / Number images used: 1277019
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.0)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7nkz


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-9fka:
Cryo-EM structure of the reduced cytochrome bd oxidase from M. tuberculosis

+
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