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- EMDB-51480: Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assemb... -

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Basic information

Entry
Database: EMDB / ID: EMD-51480
TitleCryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in ND
Map data
Sample
  • Complex: Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in ND
    • Protein or peptide: cyoB
    • Protein or peptide: cyoA
    • Protein or peptide: cyoC
    • Protein or peptide: cyoD
KeywordsElectron transport chain / Electron transfer / Heme-copper oxidase / MEMBRANE PROTEIN
Function / homology
Function and homology information


oxidoreduction-driven active transmembrane transporter activity / cytochrome o ubiquinol oxidase complex / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / ubiquinone binding / electron transport coupled proton transport / proton transmembrane transporter activity ...oxidoreduction-driven active transmembrane transporter activity / cytochrome o ubiquinol oxidase complex / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / ubiquinone binding / electron transport coupled proton transport / proton transmembrane transporter activity / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / copper ion binding / heme binding / plasma membrane
Similarity search - Function
: / Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II ...: / Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome bo(3) ubiquinol oxidase subunit 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsLindenthal M / Fu L / Staudner M / Madej MG / Ziegler C
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in ND
Authors: Lindenthal M / Staudner M / Fu L / Madej MG / Ziegler C
History
DepositionSep 4, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51480.png

Downloads & links

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Map

FileDownload / File: emd_51480.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.)
0.79 Å/pix.
x 256 pix.
= 202.01 Å		0.79 Å/pix.
x 256 pix.
= 202.01 Å		0.79 Å/pix.
x 256 pix.
= 202.01 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7891 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.204
Minimum - Maximum-0.7615285 - 1.1635414
Average (Standard dev.)0.010151172 (±0.04519795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 202.0096 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51480_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51480_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51480_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 : Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assemb...

EntireName: Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in ND
Components
  • Complex: Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in ND
    • Protein or peptide: cyoB
    • Protein or peptide: cyoA
    • Protein or peptide: cyoC
    • Protein or peptide: cyoD

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Supramolecule #1: Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assemb...

SupramoleculeName: Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in ND
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: C43
Molecular weightTheoretical: 137.62 KDa

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Macromolecule #1: cyoB

MacromoleculeName: cyoB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: ubiquinol oxidase (H+-transporting)
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFGKLSLDAV PFHEPIVMVT IAGIILGGLA LVGLITYFGK WTYLWKEWLT SVDHKRLGIM YIIVAIVMLL RGFADAIMMR SQQALASAGE AGFLPPHHYD QIFTAHGVIM IFFVAMPFVI GLMNLVVPLQ IGARDVAFPF LNNLSFWFTV VGVILVNVSL GVGEFAQTGW ...String:
MFGKLSLDAV PFHEPIVMVT IAGIILGGLA LVGLITYFGK WTYLWKEWLT SVDHKRLGIM YIIVAIVMLL RGFADAIMMR SQQALASAGE AGFLPPHHYD QIFTAHGVIM IFFVAMPFVI GLMNLVVPLQ IGARDVAFPF LNNLSFWFTV VGVILVNVSL GVGEFAQTGW LAYPPLSGIE YSPGVGVDYW IWSLQLSGIG TTLTGINFFV TILKMRAPGM TMFKMPVFTW ASLCANVLII ASFPILTVTV ALLTLDRYLG THFFTNDMGG NMMMYINLIW AWGHPEVYIL ILPVFGVFSE IAATFSRKRL FGYTSLVWAT VCITVLSFIV WLHHFFTMGA GANVNAFFGI TTMIIAIPTG VKIFNWLFTM YQGRIVFHSA MLWTIGFIVT FSVGGMTGVL LAVPGADFVL HNSLFLIAHF HNVIIGGVVF GCFAGMTYWW PKAFGFKLNE TWGKRAFWFW IIGFFVAFMP LYALGFMGMT RRLSQQIDPQ FHTMLMIAAS GAVLIALGIL CLVIQMYVSI RDRDQNRDLT GDPWGGRTLE WATSSPPPFY NFAVVPHVHE RDAFWEMKEK GEAYKKPDHY EEIHMPKNSG AGIVIAAFST IFGFAMIWHI WWLAIVGFAG MIITWIVKSF DEDVDYYVPV AEIEKLENQH FDEITKAGLK NGN

UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 1

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Macromolecule #2: cyoA

MacromoleculeName: cyoA / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRLRKYNKSL GWLSLFAGTV LLSGCNSALL DPKGQIGLEQ RSLILTAFGL MLIVVIPAIL MAVGFAWKYR ASNKDAKYSP NWSHSNKVEA VVWTVPILII IFLAVLTWKT THALEPSKPL AHDEKPITIE VVSMDWKWFF IYPEQGIATV NEIAFPANTP VYFKVTSNSV ...String:
MRLRKYNKSL GWLSLFAGTV LLSGCNSALL DPKGQIGLEQ RSLILTAFGL MLIVVIPAIL MAVGFAWKYR ASNKDAKYSP NWSHSNKVEA VVWTVPILII IFLAVLTWKT THALEPSKPL AHDEKPITIE VVSMDWKWFF IYPEQGIATV NEIAFPANTP VYFKVTSNSV MNSFFIPRLG SQIYAMAGMQ TRLHLIANEP GTYDGISASY SGPGFSGMKF KAIATPDRAA FDQWVAKAKQ SPNTMSDMAA FEKLAAPSEY NQVEYFSNVK PDLFADVINK FMAHGKSMDM TQPEGEHSAH EGMEGMDMSH AESAH

UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 2

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Macromolecule #3: cyoC

MacromoleculeName: cyoC / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MATDTLTHAT AHAHEHGHHD AGGTKIFGFW IYLMSDCILF SILFATYAVL VNGTAGGPTG KDIFELPFVL VETFLLLFSS ITYGMAAIAM YKNNKSQVIS WLALTWLFGA GFIGMEIYEF HHLIVNGMGP DRSGFLSAFF ALVGTHGLHV TSGLIWMAVL MVQIARRGLT ...String:
MATDTLTHAT AHAHEHGHHD AGGTKIFGFW IYLMSDCILF SILFATYAVL VNGTAGGPTG KDIFELPFVL VETFLLLFSS ITYGMAAIAM YKNNKSQVIS WLALTWLFGA GFIGMEIYEF HHLIVNGMGP DRSGFLSAFF ALVGTHGLHV TSGLIWMAVL MVQIARRGLT STNRTRIMCL SLFWHFLDVV WICVFTVVYL MGAM

UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 3

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Macromolecule #4: cyoD

MacromoleculeName: cyoD / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSHSTDHSGA SHGSVKTYMT GFILSIILTV IPFWMVMTGA ASPAVILGTI LAMAVVQVLV HLVCFLHMNT KSDEGWNMTA FVFTVLIIAI LVVGSIWIMW NLNYNMMMH

UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 4

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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: 8
Component:
ConcentrationNameFormula
20.0 mMKPi
150.0 mMNaClNaCl
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
TemperatureMin: 96.0 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Average exposure time: 6.0 sec. / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 99374
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software: (Name: cryoSPARC (ver. 4.4), RELION (ver. 5))
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.4)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1fft


Chain - Source name: PDB / Chain - Initial model type: experimental model

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