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- EMDB-34171: Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent -

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Basic information

Entry
Database: EMDB / ID: EMD-34171
TitleCryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent
Map data
Sample
  • Complex: Purified Escherichia coli cytochrome bo3
    • Protein or peptide: Cytochrome bo(3) ubiquinol oxidase subunit 1
    • Protein or peptide: Cytochrome bo(3) ubiquinol oxidase subunit 2
    • Protein or peptide: ubiquinol oxidase
    • Protein or peptide: Cytochrome bo(3) ubiquinol oxidase subunit 4
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME O
  • Ligand: COPPER (II) ION
  • Ligand: Ubiquinone-8
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
KeywordsCytochrome bo3 / ubiquinol oxidase / DDM detergent / TRANSLOCASE
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 / proton transmembrane transporter activity / electron transport coupled proton transport / ATP synthesis coupled electron transport ...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 / proton transmembrane transporter activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / : / aerobic respiration / electron transfer activity / copper ion binding / heme binding / plasma membrane
Similarity search - Function
: / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / 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 o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / 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/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 4 / Cytochrome bo(3) ubiquinol oxidase subunit 2
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsCao HY / Li K / Li CY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent
Authors: Cao HY / Li K / Li CY
History
DepositionAug 24, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34171.png

Downloads & links

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Map

FileDownload / File: emd_34171.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.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-1.1916983 - 1.840699
Average (Standard dev.)0.0030295646 (±0.04863576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34171_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_34171_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 : Purified Escherichia coli cytochrome bo3

EntireName: Purified Escherichia coli cytochrome bo3
Components
  • Complex: Purified Escherichia coli cytochrome bo3
    • Protein or peptide: Cytochrome bo(3) ubiquinol oxidase subunit 1
    • Protein or peptide: Cytochrome bo(3) ubiquinol oxidase subunit 2
    • Protein or peptide: ubiquinol oxidase
    • Protein or peptide: Cytochrome bo(3) ubiquinol oxidase subunit 4
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME O
  • Ligand: COPPER (II) ION
  • Ligand: Ubiquinone-8
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: Purified Escherichia coli cytochrome bo3

SupramoleculeName: Purified Escherichia coli cytochrome bo3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Cytochrome bo(3) ubiquinol oxidase subunit 1

MacromoleculeName: Cytochrome bo(3) ubiquinol oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquinol oxidase (H+-transporting)
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: S88 / ExPEC
Molecular weightTheoretical: 74.424469 KDa
SequenceString: MFGKLSLDAV PFHEPIVMVT IAGIILGGLA LVGLITYFGK WTYLWKEWLT SVDHKRLGIM YIIVAIVMLL RGFADAIMMR SQQALASAG EAGFLPPHHY DQIFTAHGVI MIFFVAMPFV IGLMNLVVPL QIGARDVAFP FLNNLSFWFT VVGVILVNVS L GVGEFAQT ...String:
MFGKLSLDAV PFHEPIVMVT IAGIILGGLA LVGLITYFGK WTYLWKEWLT SVDHKRLGIM YIIVAIVMLL RGFADAIMMR SQQALASAG EAGFLPPHHY DQIFTAHGVI MIFFVAMPFV IGLMNLVVPL QIGARDVAFP FLNNLSFWFT VVGVILVNVS L GVGEFAQT GWLAYPPLSG IEYSPGVGVD YWIWSLQLSG IGTTLTGINF FVTILKMRAP GMTMFKMPVF TWASLCANVL II ASFPILT VTVALLTLDR YLGTHFFTND MGGNMMMYIN LIWAWGHPEV YILILPVFGV FSEIAATFSR KRLFGYTSLV WAT VCITVL SFIVWLHHFF TMGAGANVNA FFGITTMIIA IPTGVKIFNW LFTMYQGRIV FHSAMLWTIG FIVTFSVGGM TGVL LAVPG ADFVLHNSLF LIAHFHNVII GGVVFGCFAG MTYWWPKAFG FKLNETWGKR AFWFWIIGFF VAFMPLYALG FMGMT RRLS QQIDPQFHTM LMIAASGAVL IALGILCLVI QMYVSIRDRD QNRDLTGDPW GGRTLEWATS SPPPFYNFAV VPHVHE RDA FWEMKEKGEA YKKPDHYEEI HMPKNSGAGI VIAAFSTIFG FAMIWHIWWL AIVGFAGMII TWIVKSFDED VDYYVPV AE IEKLENQHFD EITKAGLKNG N

UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 1

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Macromolecule #2: Cytochrome bo(3) ubiquinol oxidase subunit 2

MacromoleculeName: Cytochrome bo(3) ubiquinol oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 34.947203 KDa
SequenceString: MRLRKYNKSL GWLSLFAGTV LLSGCNSALL DPKGQIGLEQ RSLILTAFGL MLIVVIPAIL MAVGFAWKYR ASNKDAKYSP NWSHSNKVE AVVWTVPILI IIFLAVLTWK TTHALEPSKP LAHDEKPITI EVVSMDWKWF FIYPEQGIAT VNEIAFPANT P VYFKVTSN ...String:
MRLRKYNKSL GWLSLFAGTV LLSGCNSALL DPKGQIGLEQ RSLILTAFGL MLIVVIPAIL MAVGFAWKYR ASNKDAKYSP NWSHSNKVE AVVWTVPILI IIFLAVLTWK TTHALEPSKP LAHDEKPITI EVVSMDWKWF FIYPEQGIAT VNEIAFPANT P VYFKVTSN SVMNSFFIPR LGSQIYAMAG MQTRLHLIAN EPGTYDGISA SYSGPGFSGM KFKAIATPDR AAFDQWVAKA KQ SPNTMSD MAAFEKLAAP SEYNQVEYFS NVKPDLFADV INKFMAHGKS MDMTQPEGEH SAHEGMEGMD MSHAESAH

UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 2

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Macromolecule #3: ubiquinol oxidase

MacromoleculeName: ubiquinol oxidase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 22.642566 KDa
SequenceString: MATDTLTHAT AHAHEHGHHD AGGTKIFGFW IYLMSDCILF SILFATYAVL VNGTAGGPTG KDIFELPFVL VETFLLLFSS ITYGMAAIA MYKNNKSQVI SWLALTWLFG AGFIGMEIYE FHHLIVNGMG PDRSGFLSAF FALVGTHGLH VTSGLIWMAV L MVQIARRG ...String:
MATDTLTHAT AHAHEHGHHD AGGTKIFGFW IYLMSDCILF SILFATYAVL VNGTAGGPTG KDIFELPFVL VETFLLLFSS ITYGMAAIA MYKNNKSQVI SWLALTWLFG AGFIGMEIYE FHHLIVNGMG PDRSGFLSAF FALVGTHGLH VTSGLIWMAV L MVQIARRG LTSTNRTRIM CLSLFWHFLD VVWICVFTVV YLMGAM

UniProtKB: UNIPROTKB: B6HZN6

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Macromolecule #4: Cytochrome bo(3) ubiquinol oxidase subunit 4

MacromoleculeName: Cytochrome bo(3) ubiquinol oxidase subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 12.037402 KDa
SequenceString:
MSHSTDHSGA SHGSVKTYMT GFILSIILTV IPFWMVMTGA ASPAVILGTI LAMAVVQVLV HLVCFLHMNT KSDEGWNMTA FVFTVLIIA ILVVGSIWIM WNLNYNMMMH

UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 4

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Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 5 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #6: HEME O

MacromoleculeName: HEME O / type: ligand / ID: 6 / Number of copies: 1 / Formula: HEO
Molecular weightTheoretical: 838.854 Da
Chemical component information

ChemComp-HEO:
HEME O

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Macromolecule #7: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #8: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 8 / Number of copies: 1 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #9: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 9 / Number of copies: 2 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wti

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 538627
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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