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- EMDB-24265: E. coli cytochrome bo3 in MSP nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-24265
TitleE. coli cytochrome bo3 in MSP nanodisc
Map data
Sample
  • Complex: Cytochrome bo 3 ubiquinol oxidase
    • Protein or peptide: x 4 types
  • Ligand: x 9 types
KeywordsUbiquinone / Heme-copper Oxidoreductase / Electron transport / Bioenergetics / Proton pump / Membrane protein
Function / homology
Function and homology information


cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / 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 / electron transport coupled proton transport / ATP synthesis coupled electron transport / membrane => GO:0016020 / : ...cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / 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 / electron transport coupled proton transport / ATP synthesis coupled electron transport / membrane => GO:0016020 / : / aerobic respiration / 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 / Ubiquinol oxidase subunit 2, cupredoxin domain ...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
Ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsVallese F / Clarke OB
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.
Authors: Jiao Li / Long Han / Francesca Vallese / Ziqiao Ding / Sylvia K Choi / Sangjin Hong / Yanmei Luo / Bin Liu / Chun Kit Chan / Emad Tajkhorshid / Jiapeng Zhu / Oliver Clarke / Kai Zhang / Robert Gennis /
Abstract: Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) ...Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme , heme , and Cu), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75 and R71 In both structures, residue H98 occupies two conformations. In conformation 1, H98 forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 has flipped to form a hydrogen bond with E14 at the N-terminal end of TM0. We propose that H98 dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98.
History
DepositionJun 19, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.49
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.49
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n9z
  • Surface level: 0.49
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24265.png

Downloads & links

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Map

FileDownload / File: emd_24265.map.gz / Format: CCP4 / Size: 260.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.41 Å/pix.
x 407 pix.
= 168.437 Å		0.41 Å/pix.
x 377 pix.
= 156.021 Å		0.41 Å/pix.
x 445 pix.
= 184.163 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.41385 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.49 / Movie #1: 0.49
Minimum - Maximum-2.9821126 - 8.415425000000001
Average (Standard dev.)-0.000000000000409 (±0.19094658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions377445407
Spacing445377407
CellA: 184.16325 Å / B: 156.02145 Å / C: 168.43695 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.413849438202250.413848806366050.41385012285012
M x/y/z445377407
origin x/y/z0.0000.0000.000
length x/y/z184.163156.021168.437
α/β/γ90.00090.00090.000
start NX/NY/NZ127131139
NX/NY/NZ1079278
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS445377407
D min/max/mean-2.9828.415-0.000

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Supplemental data

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Additional map: #1

Fileemd_24265_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_24265_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_24265_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cytochrome bo 3 ubiquinol oxidase

EntireName: Cytochrome bo 3 ubiquinol oxidase
Components
  • Complex: Cytochrome bo 3 ubiquinol oxidase
    • Protein or peptide: Cytochrome o ubiquinol oxidase, subunit I
    • Protein or peptide: Ubiquinol oxidase subunit 2
    • Protein or peptide: Cytochrome o ubiquinol oxidase
    • Protein or peptide: Cytochrome o ubiquinol oxidase, subunit IV
  • Ligand: Ubiquinone-8
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: HEME O
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CARDIOLIPIN
  • Ligand: COPPER (II) ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Cytochrome bo 3 ubiquinol oxidase

SupramoleculeName: Cytochrome bo 3 ubiquinol oxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Cytochrome o ubiquinol oxidase, subunit I

MacromoleculeName: Cytochrome o ubiquinol oxidase, subunit I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
Source (natural)Organism: Escherichia coli (E. coli)
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: Ubiquinol oxidase subunit 2

MacromoleculeName: Ubiquinol oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
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: Ubiquinol oxidase subunit 2

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Macromolecule #3: Cytochrome o ubiquinol oxidase

MacromoleculeName: Cytochrome o ubiquinol oxidase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
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: Cytochrome bo(3) ubiquinol oxidase subunit 3

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Macromolecule #4: Cytochrome o ubiquinol oxidase, subunit IV

MacromoleculeName: Cytochrome o ubiquinol oxidase, subunit IV / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
Source (natural)Organism: Escherichia coli (E. coli)
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: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 5 / Number of copies: 1 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #6: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 6 / Number of copies: 9 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #7: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 7 / 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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Macromolecule #8: HEME O

MacromoleculeName: HEME O / type: ligand / ID: 8 / Number of copies: 1 / Formula: HEO
Molecular weightTheoretical: 838.854 Da
Chemical component information

ChemComp-HEO:
HEME O

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Macromolecule #9: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 9 / 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 #10: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 10 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #11: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 250 / 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

Concentration2.6 mg/mL
BufferpH: 7.4 / Component:
ConcentrationFormula
150.0 mMNaCl
20.0 mMHEPES
GridModel: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94681
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

1fft


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

PDB-7n9z:
E. coli cytochrome bo3 in MSP nanodisc

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