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- EMDB-53529: Cytochrome bd II oxidase qOR-2 type from Mycobacterium smegmatis -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53529
TitleCytochrome bd II oxidase qOR-2 type from Mycobacterium smegmatis
Map data
Sample
  • Complex: Cytochrome bd II oxidase
    • Protein or peptide: Cytochrome bd menaquinol oxidase subunit I
    • Protein or peptide: Cytochrome bd-I oxidase subunit II
  • Ligand: CARDIOLIPIN
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: HEME B/C
  • Ligand: MENAQUINONE-9
  • Ligand: water
KeywordsMEMBRANE PROTEIN / ACTINOBACTERIA / ELECTRON TRANSPORT
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
Cytochrome bd-I oxidase subunit II / Cytochrome bd menaquinol oxidase subunit I
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKovalova T / Janczak M / Adelroth P / Hogbom M
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2019.0043 Sweden
CitationJournal: To Be Published
Title: The qOR-2 type bd oxidase from Mycobacterium smegmatis sheds new light on functional diversity in the superfamily
Authors: Kovalova T / Janczak M / Gamiz-Hernandez AP / Lundin D / Sharma S / Vilhjalmsdottir J / Sjostrand D / Kaila V / Hogbom M / Adelroth P
History
DepositionApr 30, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53529.png

Downloads & links

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Map

FileDownload / File: emd_53529.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.208
Minimum - Maximum-0.5614102 - 1.1201259
Average (Standard dev.)-0.0016622142 (±0.029761707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_53529_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53529_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53529_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cytochrome bd II oxidase

EntireName: Cytochrome bd II oxidase
Components
  • Complex: Cytochrome bd II oxidase
    • Protein or peptide: Cytochrome bd menaquinol oxidase subunit I
    • Protein or peptide: Cytochrome bd-I oxidase subunit II
  • Ligand: CARDIOLIPIN
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: HEME B/C
  • Ligand: MENAQUINONE-9
  • Ligand: water

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Supramolecule #1: Cytochrome bd II oxidase

SupramoleculeName: Cytochrome bd II oxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

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Macromolecule #1: Cytochrome bd menaquinol oxidase subunit I

MacromoleculeName: Cytochrome bd menaquinol oxidase subunit I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 50.327875 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MVFTETLLLL AADGEPPGLL PARQQMAFSL GWHIVLACFG VAFPTMIFVV HRRGIVRDDA VALGLAQRWA KVSAVLFAIG AVSGTVLSF EMGLLWPGLM GRFGDVLGLP FAFEGLSFFV EAIFLGIYLY GWGRMPPRRH LLTLIPMGLA GIVGTFCVVS V NAWMNNPA ...String:
MVFTETLLLL AADGEPPGLL PARQQMAFSL GWHIVLACFG VAFPTMIFVV HRRGIVRDDA VALGLAQRWA KVSAVLFAIG AVSGTVLSF EMGLLWPGLM GRFGDVLGLP FAFEGLSFFV EAIFLGIYLY GWGRMPPRRH LLTLIPMGLA GIVGTFCVVS V NAWMNNPA GFRIVNGEVV DIDPWRAMFN SGVWLQFAHM WVAAFMLVGL VVSGVYAFGM LRGRVDTHHR LGFAVPFTFA SV AAVAQPL IGHVLGMRIH DTQPAKLAAF ELAQTTEGPA PLRLGGVLID GEVHWALTIP RLGSIIARNS LDAPVPGLDG VPR SDWPPV NITHLAFQSM VGIGTLLAAV AVVYWLARWR GRDLLANRWF LRLSVITGPL AVLAVESGWV ATEVGRQPWT VWKV LTTTE AASQSSGLWW SYVIVLVVYL GMTIGAVVVL RSMARRWRAG ETDLPSPYGP PRTEARS

UniProtKB: Cytochrome bd menaquinol oxidase subunit I

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Macromolecule #2: Cytochrome bd-I oxidase subunit II

MacromoleculeName: Cytochrome bd-I oxidase subunit II / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 39.166078 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTQATFVAMA MFLGVVIYAL FAGADFGSGF YDLTAGDARS GAKVRTLVDH SIGPVWEANH VWLIYILVIW WTGFPRTFAA ATTTLFIPL ALALTGIVLR GASFAFRKYS ATVSQARLFG AIFAASSLIS PFFLGTVAGA IASGRVPAEG YGDRIGSWLN P TSLVGGFL ...String:
MTQATFVAMA MFLGVVIYAL FAGADFGSGF YDLTAGDARS GAKVRTLVDH SIGPVWEANH VWLIYILVIW WTGFPRTFAA ATTTLFIPL ALALTGIVLR GASFAFRKYS ATVSQARLFG AIFAASSLIS PFFLGTVAGA IASGRVPAEG YGDRIGSWLN P TSLVGGFL AVATCVFLAG VFLTADAARS GDNGLADSLR RRTLAVGVVT GLIVFAGLYP VAHDAPTLTA GLRTYAAPLL VI ALLAGVA TVWLVFRRRY AISRIPAAVA VAAVVTGWGV GQYPWLLVDE VTIADAAGAD ATLTGLLIVV VLAGVIVLPA LAY LLRLTQ TEEWSRKLSG GSAENLYFQG WSHPQFEKGG GSGGGSGGSA WSHPQFEK

UniProtKB: Cytochrome bd-I oxidase subunit II

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Macromolecule #3: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 3 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #4: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 4 / Number of copies: 1 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

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

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Macromolecule #5: HEME B/C

MacromoleculeName: HEME B/C / type: ligand / ID: 5 / Number of copies: 2 / Formula: HEB
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEB:
HEME B/C

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Macromolecule #6: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 6 / Number of copies: 3 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 93.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200084
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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