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- EMDB-40601: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa -

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Basic information

Entry
Database: EMDB / ID: EMD-40601
Titlecytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
Map datacytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (composite structure)
Sample
  • Complex: cytochrome bc1-cbb3 supercomplex
    • Protein or peptide: x 8 types
  • Ligand: x 7 types
KeywordsElectron transport chain / Supercomplex / Pseudomonas aeruginosa / MEMBRANE PROTEIN
Function / homology
Function and homology information


cytochrome-c oxidase / plasma membrane respiratory chain complex IV / respiratory chain complex III / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain ...cytochrome-c oxidase / plasma membrane respiratory chain complex IV / respiratory chain complex III / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / intracellular membrane-bounded organelle / heme binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Cytochrome c4-like / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Cytochrome c, class IE / Cytochrome c, class IC ...Cytochrome c4-like / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Cytochrome c, class IE / Cytochrome c, class IC / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome b / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / 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. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Cytochrome c / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cbb3-type cytochrome c oxidase subunit / Cytochrome b/c1 / C-type cytochrome / Cbb3-type cytochrome c oxidase subunit II / cytochrome-c oxidase / Cytochrome b / Cytochrome C5
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsDi Trani JM / Rubinstein JL
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canadian Institutes of Health Research (CIHR)PJT451412 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure of the - respiratory supercomplex from .
Authors: Justin M Di Trani / Andreea A Gheorghita / Madison Turner / Peter Brzezinski / Pia Ädelroth / Siavash Vahidi / P Lynne Howell / John L Rubinstein /
Abstract: Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that ...Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that enables ATP synthesis and membrane transport. These protein complexes can also form higher order assemblies known as respiratory supercomplexes (SCs). The electron transport chain of the opportunistic pathogen is closely linked with its ability to invade host tissue, tolerate harsh conditions, and resist antibiotics but is poorly characterized. Here, we determine the structure of a SC that forms between the quinol:cytochrome oxidoreductase (cytochrome ) and one of the organism's terminal oxidases, cytochrome , which is found only in some bacteria. Remarkably, the SC structure also includes two intermediate electron carriers: a diheme cytochrome and a single heme cytochrome . Together, these proteins allow electron transfer from ubiquinol in cytochrome to oxygen in cytochrome . We also present evidence that different isoforms of cytochrome can participate in formation of this SC without changing the overall SC architecture. Incorporating these different subunit isoforms into the SC would allow the bacterium to adapt to different environmental conditions. Bioinformatic analysis focusing on structural motifs in the SC suggests that cytochrome - SCs also exist in other bacterial pathogens.
History
DepositionApr 26, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40601.png

Downloads & links

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Map

FileDownload / File: emd_40601.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (composite structure)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 1.24
Minimum - Maximum-7.410755 - 15.241743
Average (Standard dev.)0.001615821 (±0.18247828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions332332332
Spacing332332332
CellA=B=C: 341.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40601_additional_1.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP1 isoform, unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40601_additional_2.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cytochrome bc1 complex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40601_additional_3.map
Annotationcytochrome bc1 complex from Pseudomonas aeruginosa (Locally refined bc1 monomer with Rieske head domain in b state)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cytochrome bc1 complex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40601_additional_4.map
Annotationcytochrome bc1 complex from Pseudomonas aeruginosa (Locally refined bc1 monomer with Rieske head domain in c state, unsharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cytochrome bc1 complex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40601_additional_5.map
Annotationcytochrome bc1 complex from Pseudomonas aeruginosa (Locally refined bc1 monomer with Rieske head domain in c state, locally filtered map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa

Fileemd_40601_additional_6.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40601_additional_7.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP1 isoform, locally sharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cytochrome bc1 complex from Pseudomonas aeruginosa

Fileemd_40601_additional_8.map
Annotationcytochrome bc1 complex from Pseudomonas aeruginosa
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Half map...

Fileemd_40601_half_map_1.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Half map B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Half map...

Fileemd_40601_half_map_2.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Half map B)
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 bc1-cbb3 supercomplex

EntireName: cytochrome bc1-cbb3 supercomplex
Components
  • Complex: cytochrome bc1-cbb3 supercomplex
    • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1
    • Protein or peptide: Cytochrome c4
    • Protein or peptide: Cytochrome C5
    • Protein or peptide: cytochrome-c oxidaseCytochrome c oxidase
    • Protein or peptide: Cbb3-type Cytochrome C oxidase subunit II
    • Protein or peptide: Cbb3-type cytochrome c oxidase subunit
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: (2R)-2-(methoxymethyl)-4-{[(25R)-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
  • Ligand: HEME C
  • Ligand: COPPER (II) ION
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: cytochrome bc1-cbb3 supercomplex

SupramoleculeName: cytochrome bc1-cbb3 supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 374 kDa/nm

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Macromolecule #1: Ubiquinol-cytochrome c reductase iron-sulfur subunit

MacromoleculeName: Ubiquinol-cytochrome c reductase iron-sulfur subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 20.561396 KDa
SequenceString: NDGVNAGRRR FLVAATSVVG AAGAVGAAVP FVGSWFPSAK AKAAGAPVQV NVGKIDPGQQ IIAEWRGKPV FIVHRTKEML DALPSLEGQ LADPDSKASE QPEYVDPKLR SIKPELAVIV GICTHLGCSP TFRPEVAPAD LGPDWKGGYF CPCHGSHYDL A GRVYKGQP ...String:
NDGVNAGRRR FLVAATSVVG AAGAVGAAVP FVGSWFPSAK AKAAGAPVQV NVGKIDPGQQ IIAEWRGKPV FIVHRTKEML DALPSLEGQ LADPDSKASE QPEYVDPKLR SIKPELAVIV GICTHLGCSP TFRPEVAPAD LGPDWKGGYF CPCHGSHYDL A GRVYKGQP APLNLPIPPY TFDADDVITI GVDQEK

UniProtKB: Ubiquinol-cytochrome c reductase iron-sulfur subunit

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Macromolecule #2: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 46.111289 KDa
SequenceString: MNKFMAWVDA RFPATKMWED HLSKYYAPKN FNFWYFFGSL ALLVLVNQIL TGIWLTMSFT PSAEEAFASV EYIMRDVDYG WIIRYMHST GASAFFIVVY LHMFRGLLYG SYQKPRELVW IFGMLIYLAL MAEAFMGYLL PWGQMSYWGA QVIISLFGAI P VVGEDLAQ ...String:
MNKFMAWVDA RFPATKMWED HLSKYYAPKN FNFWYFFGSL ALLVLVNQIL TGIWLTMSFT PSAEEAFASV EYIMRDVDYG WIIRYMHST GASAFFIVVY LHMFRGLLYG SYQKPRELVW IFGMLIYLAL MAEAFMGYLL PWGQMSYWGA QVIISLFGAI P VVGEDLAQ WIRGDFLISG ITLNRFFALH VIALPIVLLG LVVLHILALH EVGSNNPDGV DIKKKKDENG VPLDGIAFHP YY TVKDIVG VVVFLFIFCT VIFFFPEMGG YFLEKPNFEM ANQFKTPEHI APVWYFTPFY AILRAVPDKL MGVVAMGAAI AVL FVLPWL DRSPVRSIRY KGWLSKLWLV IFAVSFVILG YYGAQAPSPL GTTLSRVCTV LYFAFFILMP FYTRMEKTKP VPER VTG

UniProtKB: Cytochrome b

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Macromolecule #3: Cytochrome c1

MacromoleculeName: Cytochrome c1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 26.280209 KDa
SequenceString: PQLDHVDIDL TDKAAMQDGA RTFANYCMGC HSAKFQRYER VATDLGIPAD LMMEKLVFTG AKIGDHMDIG MKPADAKTWF GAAPPDLTL VARVRGTDWL YSYLRSFYED PKRPWGVNNV IFPNVGMPNV LAPLQGRQVI GCKQVQVVED GKKQFDPLTG T PLTHEACD ...String:
PQLDHVDIDL TDKAAMQDGA RTFANYCMGC HSAKFQRYER VATDLGIPAD LMMEKLVFTG AKIGDHMDIG MKPADAKTWF GAAPPDLTL VARVRGTDWL YSYLRSFYED PKRPWGVNNV IFPNVGMPNV LAPLQGRQVI GCKQVQVVED GKKQFDPLTG T PLTHEACD QLTVVPKTGE LNEAQFDEKV KNLVTFLAYS ANPNKLASER IGTYVLLYLA FFFVFAYLLK REYWK

UniProtKB: Cytochrome b/c1

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Macromolecule #4: Cytochrome c4

MacromoleculeName: Cytochrome c4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 18.6961 KDa
SequenceString:
AGDAAAGQAK AAVCGACHGA DGNSPAPNFP KLAGQGERYL LKQMHDIKDG KRTVLEMTGL LTNLSDQDLA DIAAYFASQK MSVGMADPN LVAQGEALFR GGKIAEGMPA CTGCHSPSGV GIATAGFPHL GGQHATYVAK QLTDFREGTR TNDGDTKIMQ S IAAKLSNK DIAAISSYIQ GLH

UniProtKB: C-type cytochrome

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Macromolecule #5: Cytochrome C5

MacromoleculeName: Cytochrome C5 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 13.475439 KDa
SequenceString:
MLAAQAAVLA LWAVSAQATT TDDAIAKRLE PVGKVCVQGK ECEGVGAVAA AAGGGGARSG EDIVGKTCNT CHGTGLLGAP KVGDKAEWG KRAKEQGGLD GLLAKAISGI NAMPPKGTCA DCSDDELKAA IKHMSGL

UniProtKB: Cytochrome C5

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Macromolecule #6: cytochrome-c oxidase

MacromoleculeName: cytochrome-c oxidase / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 52.586527 KDa
SequenceString: PAYNYKVVRQ FAIMTVVWGV IGMGLGVLIA SQLVWPQMNF DLPWTSFGRL RPLHTNLVIF AFGGCALFAT SYYTVQRTCQ VRLFSDTLA AFTFWGWQAV AVILLVSLPL GNTTTKEYAE IEFTGAIWLA IVWVAYAVVF FGTLIKRKVK HIYVGNWFFG S FILTTAML ...String:
PAYNYKVVRQ FAIMTVVWGV IGMGLGVLIA SQLVWPQMNF DLPWTSFGRL RPLHTNLVIF AFGGCALFAT SYYTVQRTCQ VRLFSDTLA AFTFWGWQAV AVILLVSLPL GNTTTKEYAE IEFTGAIWLA IVWVAYAVVF FGTLIKRKVK HIYVGNWFFG S FILTTAML HIVNHMSLPV SWFKSYSMYS GATDAMVQWW YGHNAVGFFL TTGFLGMMYY FVPKQAGRPV YSYRLSIVHF WA LITLYIW AGPHHLHYTA LPDWAQSLGM VMSLILLAPS WGGMINGMMT LSGAWHKLRD DPILRFLVVS LAFYGMSTFE GPM MAIKTV NALSHYTDWT IGHVHAGALG WVAMITIGSL YHLIPKVYGV EKMHSVGLIN AHFWLATIGT VLYIASLWVN GITQ GLMWR AVNEDGTLTY SFVESLVASH PGFIVRLVGG GFFLTGMLLM SYNTWRTVRQ ARPEGILAAA RMA

UniProtKB: cytochrome-c oxidase

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Macromolecule #7: Cbb3-type Cytochrome C oxidase subunit II

MacromoleculeName: Cbb3-type Cytochrome C oxidase subunit II / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 22.417715 KDa
SequenceString: MKNHEILEKN VGLLAIFMVI AVSIGGLTQI VPLFFQDVTN TPVEGMKPRT ALELEGRDIY IREGCVGCHS QMVRPFRAET ERYGHYSVA GESVWDHPFL WGSKRTGPDL ARVGGRYSDD WHRAHLYNPR NVVPESKMPA YPWLVENKLD GKDTATKMEV L RKLGVPYT ...String:
MKNHEILEKN VGLLAIFMVI AVSIGGLTQI VPLFFQDVTN TPVEGMKPRT ALELEGRDIY IREGCVGCHS QMVRPFRAET ERYGHYSVA GESVWDHPFL WGSKRTGPDL ARVGGRYSDD WHRAHLYNPR NVVPESKMPA YPWLVENKLD GKDTATKMEV L RKLGVPYT DEDIAGAREA VKGKTEMDAL VAFLQGLGTS IK

UniProtKB: Cbb3-type cytochrome c oxidase subunit II

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Macromolecule #8: Cbb3-type cytochrome c oxidase subunit

MacromoleculeName: Cbb3-type cytochrome c oxidase subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 34.078703 KDa
SequenceString: MTTFWSLYIT ALTLGTLLAL TWLIFATRKG QRSSTTDETV GHSYDGIEEY DNPLPKWWFM LFVGTLVFAV GYLALYPGLG TWKGLMPGY QSADEFADKE KGWTGVHQWE KEMAKADEKY GPIFAKFAAM PIEEVAKDPQ AVKMGGRLFA SNCSICHGSD A KGAYGFPN ...String:
MTTFWSLYIT ALTLGTLLAL TWLIFATRKG QRSSTTDETV GHSYDGIEEY DNPLPKWWFM LFVGTLVFAV GYLALYPGLG TWKGLMPGY QSADEFADKE KGWTGVHQWE KEMAKADEKY GPIFAKFAAM PIEEVAKDPQ AVKMGGRLFA SNCSICHGSD A KGAYGFPN LTDADWRWGG EPETIKTTIM AGRHAAMPAW GEVIGEEGVK NVAAFVLTQM DGRKLPEGAK ADIEAGKQVF AT TCVACHG PEGKGTPAMG APDLTHPGAF IYGSSFAQLQ QTIRYGRQGV MPAQQEHLGN DKVHLLAAYV YSLSH

UniProtKB: Cbb3-type cytochrome c oxidase subunit

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Macromolecule #9: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 9 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Macromolecule #10: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 10 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #11: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 11 / Number of copies: 2 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

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Macromolecule #12: (2R)-2-(methoxymethyl)-4-{[(25R)-spirost-5-en-3beta-yl]oxy}butyl ...

MacromoleculeName: (2R)-2-(methoxymethyl)-4-{[(25R)-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
type: ligand / ID: 12 / Number of copies: 2 / Formula: I7Y
Molecular weightTheoretical: 855.06 Da
Chemical component information

ChemComp-I7Y:
(2R)-2-(methoxymethyl)-4-{[(25R)-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside

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Macromolecule #13: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 13 / Number of copies: 9 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #14: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

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Macromolecule #15: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 15 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48594

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