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- EMDB-13108: High resolution structure of cytochrome bd-II oxidase from E. coli -

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Basic information

Entry
Database: EMDB / ID: EMD-13108
TitleHigh resolution structure of cytochrome bd-II oxidase from E. coli
Map dataFull map
Sample
  • Complex: Cytochrome bd-II oxidase from E. coli composed of subunit AppB, AppC and AppX
    • Protein or peptide: Cytochrome bd-II ubiquinol oxidase subunit 2
    • Protein or peptide: Cytochrome bd-II ubiquinol oxidase subunit 1
    • Protein or peptide: Putative cytochrome bd-II ubiquinol oxidase subunit AppX
  • Ligand: CARDIOLIPIN
  • Ligand: 2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl]naphthalene-1,4-dione
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: HEME B/C
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: OXYGEN MOLECULEAllotropes of oxygen
  • Ligand: water
Function / homology
Function and homology information


ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / cytochrome complex / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cell outer membrane / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Membrane bound YbgT-like / Membrane bound YbgT-like protein / 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
Putative cytochrome bd-II ubiquinol oxidase subunit AppX / Cytochrome bd-II ubiquinol oxidase subunit 2 / Cytochrome bd-II ubiquinol oxidase subunit 1
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.06 Å
AuthorsGrund TN / Wu D / Bald D / Michel H / Safarian S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck SocietyNobel laureate fellowship Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Mechanistic and structural diversity between cytochrome isoforms of .
Authors: Tamara N Grund / Melanie Radloff / Di Wu / Hojjat G Goojani / Luca F Witte / Wiebke Jösting / Sabine Buschmann / Hannelore Müller / Isam Elamri / Sonja Welsch / Harald Schwalbe / Hartmut ...Authors: Tamara N Grund / Melanie Radloff / Di Wu / Hojjat G Goojani / Luca F Witte / Wiebke Jösting / Sabine Buschmann / Hannelore Müller / Isam Elamri / Sonja Welsch / Harald Schwalbe / Hartmut Michel / Dirk Bald / Schara Safarian /
Abstract: The treatment of infectious diseases caused by multidrug-resistant pathogens is a major clinical challenge of the 21st century. The membrane-embedded respiratory cytochrome -type oxygen reductase is ...The treatment of infectious diseases caused by multidrug-resistant pathogens is a major clinical challenge of the 21st century. The membrane-embedded respiratory cytochrome -type oxygen reductase is a critical survival factor utilized by pathogenic bacteria during infection, proliferation and the transition from acute to chronic states. encodes for two cytochrome isoforms that are both involved in respiration under oxygen limited conditions. Mechanistic and structural differences between () and () operon encoded cytochrome variants have remained elusive in the past. Here, we demonstrate that cytochrome - catalyzes oxidation of benzoquinols while possessing additional specificity for naphthoquinones. Our data show that although menaquinol-1 (MK1) is not able to directly transfer electrons onto cytochrome from , it has a stimulatory effect on its oxygen reduction rate in the presence of ubiquinol-1. We further determined cryo-EM structures of cytochrome - to high resolution of 2.1 Å. Our structural insights confirm that the general architecture and substrate accessible pathways are conserved between the two oxidase isoforms, but two notable differences are apparent upon inspection: (i) does not contain a CydH-like subunit, thereby exposing heme to the membrane environment and (ii) the AppB subunit harbors a structural demethylmenaquinone-8 molecule instead of ubiquinone-8 as found in CydB of Our work completes the structural landscape of terminal respiratory oxygen reductases of and suggests that structural and functional properties of the respective oxidases are linked to quinol-pool dependent metabolic adaptations in .
History
DepositionJun 23, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oy2
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13108.png

Downloads & links

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Map

FileDownload / File: emd_13108.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.061831966 - 0.16589892
Average (Standard dev.)-4.043137e-05 (±0.0027392483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.272 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z214.272214.272214.272
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0620.166-0.000

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Supplemental data

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Half map: Half map

Fileemd_13108_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_13108_half_map_2.map
AnnotationHalf 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 from E. coli composed of subunit AppB, A...

EntireName: Cytochrome bd-II oxidase from E. coli composed of subunit AppB, AppC and AppX
Components
  • Complex: Cytochrome bd-II oxidase from E. coli composed of subunit AppB, AppC and AppX
    • Protein or peptide: Cytochrome bd-II ubiquinol oxidase subunit 2
    • Protein or peptide: Cytochrome bd-II ubiquinol oxidase subunit 1
    • Protein or peptide: Putative cytochrome bd-II ubiquinol oxidase subunit AppX
  • Ligand: CARDIOLIPIN
  • Ligand: 2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl]naphthalene-1,4-dione
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: HEME B/C
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
  • Ligand: OXYGEN MOLECULEAllotropes of oxygen
  • Ligand: water

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Supramolecule #1: Cytochrome bd-II oxidase from E. coli composed of subunit AppB, A...

SupramoleculeName: Cytochrome bd-II oxidase from E. coli composed of subunit AppB, AppC and AppX
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 104 KDa

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Macromolecule #1: Cytochrome bd-II ubiquinol oxidase subunit 2

MacromoleculeName: Cytochrome bd-II ubiquinol oxidase subunit 2 / 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)
Molecular weightTheoretical: 42.448543 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MFDYETLRFI WWLLIGVILV VFMISDGFDM GIGCLLPLVA RNDDERRIVI NSVGAHWEGN QVWLILAGGA LFAAWPRVYA AAFSGFYVA MILVLCSLFF RPLAFDYRGK IADARWRKMW DAGLVIGSLV PPVVFGIAFG NLLLGVPFAF TPQLRVEYLG S FWQLLTPF ...String:
MFDYETLRFI WWLLIGVILV VFMISDGFDM GIGCLLPLVA RNDDERRIVI NSVGAHWEGN QVWLILAGGA LFAAWPRVYA AAFSGFYVA MILVLCSLFF RPLAFDYRGK IADARWRKMW DAGLVIGSLV PPVVFGIAFG NLLLGVPFAF TPQLRVEYLG S FWQLLTPF PLLCGLLSLG MVILQGGVWL QLKTVGVIHL RSQLATKRAA LLVMLCFLLA GYWLWVGIDG FVLLAQDANG PS NPLMKLV AVLPGAWMNN FVESPVLWIF PLLGFFCPLL TVMAIYRGRP GWGFLMASLM QFGVIFTAGI TLFPFVMPSS VSP ISSLTL WDSTSSQLTL SIMLVIVLIF LPIVLLYTLW SYYKMWGRMT TETLRRNENE LY

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Macromolecule #2: Cytochrome bd-II ubiquinol oxidase subunit 1

MacromoleculeName: Cytochrome bd-II ubiquinol oxidase subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquinol oxidase (H+-transporting)
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 57.962469 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MWDVIDLSRW QFALTALYHF LFVPLTLGLI FLLAIMETIY VVTGKTIYRD MTRFWGKLFG INFALGVATG LTMEFQFGTN WSFYSNYVG DIFGAPLAME ALMAFFLEST FVGLFFFGWQ RLNKYQHLLV TWLVAFGSNL SALWILNANG WMQYPTGAHF D IDTLRMEM ...String:
MWDVIDLSRW QFALTALYHF LFVPLTLGLI FLLAIMETIY VVTGKTIYRD MTRFWGKLFG INFALGVATG LTMEFQFGTN WSFYSNYVG DIFGAPLAME ALMAFFLEST FVGLFFFGWQ RLNKYQHLLV TWLVAFGSNL SALWILNANG WMQYPTGAHF D IDTLRMEM TSFSELVFNP VSQVKFVHTV MAGYVTGAMF IMAISAWYLL RGRERNVALR SFAIGSVFGT LAIIGTLQLG DS SAYEVAQ VQPVKLAAME GEWQTEPAPA PFHVVAWPEQ DQERNAFALK IPALLGILAT HSLDKPVPGL KNLMAETYPR LQR GRMAWL LMQEISQGNR EPHVLQAFRG LEGDLGYGML LSRYAPDMNH VTAAQYQAAM RGAIPQVAPV FWSFRIMVGC GSLL LLVML IALVQTLRGK IDQHRWVLKM ALWSLPLPWI AIEAGWFMTE FGRQPWAIQD ILPTYSAHSA LTTGQLAFSL IMIVG LYTL FLIAEVYLMQ KYARLGPSAM QSEQPTQQQG

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Macromolecule #3: Putative cytochrome bd-II ubiquinol oxidase subunit AppX

MacromoleculeName: Putative cytochrome bd-II ubiquinol oxidase subunit AppX
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 6.43634 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MWYLLWFVGI LLMCSLSTLV LVWLDPRLKS IEGRGTSGSS GSGSGGSGSG GGGWSHPQFE K

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Macromolecule #4: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 4 / Number of copies: 1 / Formula: CDN
Molecular weightTheoretical: 1.151511 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #5: 2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3,7,11,15,19,...

MacromoleculeName: 2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl]naphthalene-1,4-dione
type: ligand / ID: 5 / Number of copies: 1 / Formula: DK8
Molecular weightTheoretical: 703.09 Da
Chemical component information

ChemComp-DK8:
2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl]naphthalene-1,4-dione

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Macromolecule #6: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 6 / Number of copies: 1 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

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Macromolecule #7: HEME B/C

MacromoleculeName: HEME B/C / type: ligand / ID: 7 / Number of copies: 2 / Formula: HEB
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEB:
HEME B/C

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Macromolecule #8: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 8 / Number of copies: 1 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

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

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Macromolecule #9: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 9 / Number of copies: 1 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE / Allotropes of oxygen

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

Concentration1.5 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMTris
100.0 mMNaClSodium chloride
0.002 % (w/v)LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / 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

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 108.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 533309
FSC plot (resolution estimation)

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