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- EMDB-10340: The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae -

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Basic information

Entry
Database: EMDB / ID: EMD-10340
TitleThe III2-IV(5B)2 respiratory supercomplex from S. cerevisiae
Map dataIII2-IV5B2 respiratory supercomplex from S. cerevisiae
Sample
  • Complex: The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae
    • Protein or peptide: x 23 types
Function / homology
Function and homology information


: / Complex III assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : ...: / Complex III assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / : / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / nuclear periphery / proton transmembrane transport / mitochondrial membrane / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / membrane / metal ion binding / cytosol
Similarity search - Function
Respiratory supercomplex factor 2, mitochondrial / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. ...Respiratory supercomplex factor 2, mitochondrial / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / 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 b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c/quinol oxidase subunit II / : / Cytochrome b / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / : / 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 c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16)
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial ...Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8, mitochondrial / Cytochrome c oxidase subunit 7, mitochondrial / Cytochrome b-c1 complex subunit 9, mitochondrial / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome b-c1 complex subunit 10, mitochondrial / Respiratory supercomplex factor 2, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 26, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMarechal A / Hartley A / Pinotsis N
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M00936X/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes.
Authors: Andrew M Hartley / Brigitte Meunier / Nikos Pinotsis / Amandine Maréchal /
Abstract: The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, ...The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, remain to be determined. In , cytochrome oxidase (CIV) forms SCs of varying stoichiometry with cytochrome (CIII). Recent studies have revealed, in normoxic growth conditions, an interface made exclusively by Cox5A, the only yeast respiratory protein that exists as one of two isoforms depending on oxygen levels. Here we present the cryo-EM structures of the III-IV and III-IV SCs containing the hypoxic isoform Cox5B solved at 3.4 and 2.8 Å, respectively. We show that the change of isoform does not affect SC formation or activity, and that SC stoichiometry is dictated by the level of CIII/CIV biosynthesis. Comparison of the CIV- and CIV-containing SC structures highlighted few differences, found mainly in the region of Cox5. Additional density was revealed in all SCs, independent of the CIV isoform, in a pocket formed by Cox1, Cox3, Cox12, and Cox13, away from the CIII-CIV interface. In the CIV-containing hypoxic SCs, this could be confidently assigned to the hypoxia-induced gene 1 (Hig1) type 2 protein Rcf2. With conserved residues in mammalian Hig1 proteins and Cox3/Cox12/Cox13 orthologs, we propose that Hig1 type 2 proteins are stoichiometric subunits of CIV, at least when within a III-IV SC.
History
DepositionSep 26, 2019-
Header (metadata) releaseApr 22, 2020-
Map releaseApr 22, 2020-
UpdateMay 13, 2020-
Current statusMay 13, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t0b
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10340.png

Downloads & links

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Map

FileDownload / File: emd_10340.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIII2-IV5B2 respiratory supercomplex from S. cerevisiae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 448 pix.
= 486.08 Å		1.09 Å/pix.
x 448 pix.
= 486.08 Å		1.09 Å/pix.
x 448 pix.
= 486.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24 / Movie #1: 0.4
Minimum - Maximum-1.7427498 - 3.0284133
Average (Standard dev.)0.0014867621 (±0.0718099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 486.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z486.080486.080486.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-1.7433.0280.001

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Supplemental data

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Sample components

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Entire : The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae

EntireName: The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae
Components
  • Complex: The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae
    • Protein or peptide: Cox1 Cytochrome c oxidase subunit 1
    • Protein or peptide: Cox2 Cytochrome c oxidase subunit 2
    • Protein or peptide: Cox3 Cytochrome c oxidase subunit 3
    • Protein or peptide: Cox4 Cytochrome c oxidase subunit 4
    • Protein or peptide: Cox5B Cytochrome c oxidase subunit 5B
    • Protein or peptide: Cox6 Cytochrome c oxidase subunit 6
    • Protein or peptide: Cox7 Cytochrome c oxidase subunit 7
    • Protein or peptide: Cox8 Cytochrome c oxidase polypeptide VIII
    • Protein or peptide: Cox9 Cytochrome c oxidase subunit 7A
    • Protein or peptide: Cox12 Cytochrome c oxidase subunit 6B
    • Protein or peptide: Cox13 Cytochrome c oxidase subunit 6A
    • Protein or peptide: Cox26, Uncharacterized protein YDR119W-A
    • Protein or peptide: RCF2, Respiratory supercomplex factor 2, mitochondrial
    • Protein or peptide: Qcr1 CYTOCHROME B-C1 COMPLEX SUBUNIT 1
    • Protein or peptide: Qcr2 CYTOCHROME B-C1 COMPLEX SUBUNIT 2
    • Protein or peptide: CYTOCHROME b
    • Protein or peptide: CYTOCHROME c1
    • Protein or peptide: CYTOCHROME b-c1 COMPLEX SUBUNIT RIESKE
    • Protein or peptide: CYTOCHROME b-c1 COMPLEX SUBUNIT 6
    • Protein or peptide: CYTOCHROME b-c1 COMPLEX SUBUNIT 7
    • Protein or peptide: CYTOCHROME b-c1 COMPLEX SUBUNIT 8
    • Protein or peptide: CYTOCHROME b-c1 COMPLEX SUBUNIT 9
    • Protein or peptide: CYTOCHROME b-c1 COMPLEX SUBUNIT 10

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Supramolecule #1: The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae

SupramoleculeName: The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Contains two copies of Complex III and two copies of Complex IV (Cox1,Cox2,Cox3,Cox4,Cox5B,Cox6,Cox7,Cox8,Cox9,Cox12,Cox13,Cox26 and Rcf2
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Cox1 Cytochrome c oxidase subunit 1

MacromoleculeName: Cox1 Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFF LVMPALIGGF GNYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV E SGAGTGWT VYPPLSSIQA HSGPSVDLAI FALHLTSISS LLGAINFIVT ...String:
MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFF LVMPALIGGF GNYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV E SGAGTGWT VYPPLSSIQA HSGPSVDLAI FALHLTSISS LLGAINFIVT TLNMRTNGMT MH KLPLFVW SIFITAFLLL LSLPVLSAGI TMLLLDRNFN TSFFEVSGGG DPILYEHLFW FFG HPEVYI LIIPGFGIIS HVVSTYSKKP VFGEISMVYA MASIGLLGFL VWSHHMYIVG LDAD TRAYF TSATMIIAIP TGIKIFSWLA TIHGGSIRLA TPMLYAIAFL FLFTMGGLTG VALAN ASLD VAFHDTYYVV GHFHYVLSMG AIFSLFAGYY YWSPQILGLN YNEKLAQIQF WLIFIG ANV IFFPMHFLGI NGMPRRIPDY PDAFAGWNYV ASIGSFIATL SLFLFIYILY DQLVNGL NN KVNNKSVIYN KAPDFVESNT IFNLNTVKSS SIEFLLTSPP AVHSFNTPAV QS

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Macromolecule #3: Cox2 Cytochrome c oxidase subunit 2

MacromoleculeName: Cox2 Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MLDLLRLQLT TFIMNDVPTP YACYFQDSAT PNQEGILELH DNIMFYLLVI LGLVSWMLYT IVMTYSKNP IAYKYIKHGQ TIEVIWTIFP AVILLIIAFP SFILLYLCDE VISPAMTIKA I GYQWYWKY EYSDFINDSG ETVEFESYVI PDELLEEGQL RLLDTDTSMV ...String:
MLDLLRLQLT TFIMNDVPTP YACYFQDSAT PNQEGILELH DNIMFYLLVI LGLVSWMLYT IVMTYSKNP IAYKYIKHGQ TIEVIWTIFP AVILLIIAFP SFILLYLCDE VISPAMTIKA I GYQWYWKY EYSDFINDSG ETVEFESYVI PDELLEEGQL RLLDTDTSMV VPVDTHIRFV VT AADVIHD FAIPSLGIKV DATPGRLNQV SALIQREGVF YGACSELCGT GHANMPIKIE AVS LPKFLE WLNEQ

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Macromolecule #4: Cox3 Cytochrome c oxidase subunit 3

MacromoleculeName: Cox3 Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDI VAEATYLGDH TMAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT L GACWPPVG IEAVQPTELP LLNTIILLSS GATVTYSHHA LIAGNRNKAL ...String:
MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDI VAEATYLGDH TMAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT L GACWPPVG IEAVQPTELP LLNTIILLSS GATVTYSHHA LIAGNRNKAL SGLLITFWLI VI FVTCQYI EYTNAAFTIS DGVYGSVFYA GTGLHFLHMV MLAAMLGVNY WRMRNYHLTA GHH VGYETT IIYTHVLDVI WLFLYVVFYW WGV

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Macromolecule #5: Cox4 Cytochrome c oxidase subunit 4

MacromoleculeName: Cox4 Cytochrome c oxidase subunit 4 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MLSLRQSIRF FKPATRTLCS SRYLLQQKPV VKTAQNLAEV NGPETLIGPG AKEGTVPTDL DQETGLARL ELLGKLEGID VFDTKPLDSS RKGTMKDPII IESYDDYRYV GCTGSPAGSH T IMWLKPTV NEVARCWECG SVYKLNPVGV PNDDHHH

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Macromolecule #6: Cox5B Cytochrome c oxidase subunit 5B

MacromoleculeName: Cox5B Cytochrome c oxidase subunit 5B / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MLRTSLTKGA RLTGTRFVQT KALSKATLTD LPERWENMPN LEQKEIADNL TERQKLPWKT LNNEEIKAA WYISYGEWGP RRPVHGKGDV AFITKGVFLG LGISFGLFGL VRLLANPETP K TMNREWQL KSDEYLKSKN ANPWGGYSQV QSK

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Macromolecule #7: Cox6 Cytochrome c oxidase subunit 6

MacromoleculeName: Cox6 Cytochrome c oxidase subunit 6 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MLSRAIFRNP VINRTLLRAR PGAYHATRLT KNTFIQSRKY SDAHDEETFE EFTARYEKEF DEAYDLFEV QRVLNNCFSY DLVPAPAVIE KALRAARRVN DLPTAIRVFE ALKYKVENED Q YKAYLDEL KDVRQELGVP LKEELFPSSS

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Macromolecule #8: Cox7 Cytochrome c oxidase subunit 7

MacromoleculeName: Cox7 Cytochrome c oxidase subunit 7 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MANKVIQLQK IFQSSTKPLW WRHPRSALYL YPFYAIFAVA VVTPLLYIPN AIRGIKAKKA

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Macromolecule #9: Cox8 Cytochrome c oxidase polypeptide VIII

MacromoleculeName: Cox8 Cytochrome c oxidase polypeptide VIII / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MLCQQMIRTT AKRSSNIMTR PIIMKRSVHF KDGVYENIPF KVKGRKTPYA LSHFGFFAIG FAVPFVACY VQLKKSGAF

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Macromolecule #10: Cox9 Cytochrome c oxidase subunit 7A

MacromoleculeName: Cox9 Cytochrome c oxidase subunit 7A / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MTIAPITGTI KRRVIMDIVL GFSLGGVMAS YWWWGFHMDK INKREKFYAE LAERKKQEN

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Macromolecule #11: Cox12 Cytochrome c oxidase subunit 6B

MacromoleculeName: Cox12 Cytochrome c oxidase subunit 6B / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MADQENSPLH TVGFDARFPQ QNQTKHCWQS YVDYHKCVNM KGEDFAPCKV FWKTYNALCP LDWIEKWDD QREKGIFAGD INSD

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Macromolecule #12: Cox13 Cytochrome c oxidase subunit 6A

MacromoleculeName: Cox13 Cytochrome c oxidase subunit 6A / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MFRQCAKRYA SSLPPNALKP AFGPPDKVAA QKFKESLMAT EKHAKDTSNM WVKISVWVAL PAIALTAVN TYFVEKEHAE HREHLKHVPD SEWPRDYEFM NIRSKPFFWG DGDKTLFWNP V VNRHIEHD DG ARGSHHH HHH

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Macromolecule #13: Cox26, Uncharacterized protein YDR119W-A

MacromoleculeName: Cox26, Uncharacterized protein YDR119W-A / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MFRQCAKRYA SSLPPNALKP AFGPPDKVAA QKFKESLMAT EKHAKDTSNM WVKISVWVAL PAIALTAVN TYFVEKEHAE HREHLKHVPD SEWPRDYEFM NIRSKPFFWG DGDKTLFWNP V VNRHIEHD DG ARGSHHH HHH

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Macromolecule #14: RCF2, Respiratory supercomplex factor 2, mitochondrial

MacromoleculeName: RCF2, Respiratory supercomplex factor 2, mitochondrial
type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MKILTQDEIE AHRSHTLKGG IEGALAGFAI SAIIFKVLPR RYPKFKPSTL TWSIKTALWI TPPTVLTAI CAEEASNNFD ATMYGSGSSS EDALDEHRRW KSLSTKDKFV EGLSNNKYKI I TGAWAASL YGSWVIVNKD PIMTKAQKIV QARMYAQFIT VGLLLASVGL ...String:
MKILTQDEIE AHRSHTLKGG IEGALAGFAI SAIIFKVLPR RYPKFKPSTL TWSIKTALWI TPPTVLTAI CAEEASNNFD ATMYGSGSSS EDALDEHRRW KSLSTKDKFV EGLSNNKYKI I TGAWAASL YGSWVIVNKD PIMTKAQKIV QARMYAQFIT VGLLLASVGL SMYENKLHPN KQ KVNEMRR WENALRVAEE EERLEKEGRR TGYVSNEERI NSKIFKS

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Macromolecule #15: Qcr1 CYTOCHROME B-C1 COMPLEX SUBUNIT 1

MacromoleculeName: Qcr1 CYTOCHROME B-C1 COMPLEX SUBUNIT 1 / type: protein_or_peptide / ID: 15 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MLRTVTSKTV SNQFKRSLAT AVATPKAEVT QLSNGIVVAT EHNPSAHTAS VGVVFGSGAA NENPYNNGV SNLWKNIFLS KENSAVAAKE GLALSSNISR DFQSYIVSSL PGSTDKSLDF L NQSFIQQK ANLLSSSNFE ATKKSVLKQV QDFEENDHPN RVLEHLHSTA ...String:
MLRTVTSKTV SNQFKRSLAT AVATPKAEVT QLSNGIVVAT EHNPSAHTAS VGVVFGSGAA NENPYNNGV SNLWKNIFLS KENSAVAAKE GLALSSNISR DFQSYIVSSL PGSTDKSLDF L NQSFIQQK ANLLSSSNFE ATKKSVLKQV QDFEENDHPN RVLEHLHSTA FQNTPLSLPT RG TLESLEN LVVADLESFA NNHFLNSNAV VVGTGNIKHE DLVNSIESKN LSLQTGTKPV LKK KAAFLG SEVRLRDDTL PKAWISLAVE GEPVNSPNYF VAKLAAQIFG SYNAFEPASR LQGI KLLDN IQEYQLCDNF NHFSLSYKDS GLWGFSTATR NVTMIDDLIH FTLKQWNRLT ISVTD TEVE RAKSLLKLQL GQLYESGNPV NDANLLGAEV LIKGSKLSLG EAFKKIDAIT VKDVKA WAG KRLWDQDIAI AGTGQIEGLL DYMRIRSDMS MMRW

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Macromolecule #16: Qcr2 CYTOCHROME B-C1 COMPLEX SUBUNIT 2

MacromoleculeName: Qcr2 CYTOCHROME B-C1 COMPLEX SUBUNIT 2 / type: protein_or_peptide / ID: 16 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MLSAARLQFA QGSVRRLTVS ARDAPTKIST LAVKVHGGSR YATKDGVAHL LNRFNFQNTN TRSALKLVR ESELLGGTFK STLDREYITL KATFLKDDLP YYVNALADVL YKTAFKPHEL T ESVLPAAR YDYAVAEQCP VKSAEDQLYA ITFRKGLGNP LLYDGVERVS ...String:
MLSAARLQFA QGSVRRLTVS ARDAPTKIST LAVKVHGGSR YATKDGVAHL LNRFNFQNTN TRSALKLVR ESELLGGTFK STLDREYITL KATFLKDDLP YYVNALADVL YKTAFKPHEL T ESVLPAAR YDYAVAEQCP VKSAEDQLYA ITFRKGLGNP LLYDGVERVS LQDIKDFADK VY TKENLEV SGENVVEADL KRFVDESLLS TLPAGKSLVS KSEPKFFLGE ENRVRFIGDS VAA IGIPVN KASLAQYEVL ANYLTSALSE LSGLISSAKL DKFTDGGLFT LFVRDQDSAV VSSN IKKIV ADLKKGKDLS PAINYTKLKN AVQNESVSSP IELNFDAVKD FKLGKFNYVA VGDVS NLPY LDEL

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Macromolecule #17: CYTOCHROME b

MacromoleculeName: CYTOCHROME b / type: protein_or_peptide / ID: 17 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MAFRKSNVYL SLVNSYIIDS PQPSSINYWW NMGSLLGLCL VIQIVTGIFM AMHYSSNIEL AFSSVEHIM RDVHNGYILR YLHANGASFF FMVMFMHMAK GLYYGSYRSP RVTLWNVGVI I FILTIATA FLGYCCVYGQ MSHWGATVIT NLFSAIPFVG NDIVSWLWGG ...String:
MAFRKSNVYL SLVNSYIIDS PQPSSINYWW NMGSLLGLCL VIQIVTGIFM AMHYSSNIEL AFSSVEHIM RDVHNGYILR YLHANGASFF FMVMFMHMAK GLYYGSYRSP RVTLWNVGVI I FILTIATA FLGYCCVYGQ MSHWGATVIT NLFSAIPFVG NDIVSWLWGG FSVSNPTIQR FF ALHYLVP FIIAAMVIMH LMALHIHGSS NPLGITGNLD RIPMHSYFIF KDLVTVFLFM LIL ALFVFY SPNTLGHPDN YIPGNPLVTP ASIVPEWYLL PFYAILRSIP DKLLGVITMF AAIL VLLVL PFTDRSVVRG NTFKVLSKFF FFIFVFNFVL LGQIGACHVE VPYVLMGQIA TFIYF AYFL IIVPVISTIE NVLFYIGRVN K

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Macromolecule #18: CYTOCHROME c1

MacromoleculeName: CYTOCHROME c1 / type: protein_or_peptide / ID: 18 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MFSNLSKRWA QRTLSKSFYS TATGAASKSG KLTQKLVTAG VAAAGITAST LLYADSLTAE AMTAAEHGL HAPAYAWSHN GPFETFDHAS IRRGYQVYRE VCAACHSLDR VAWRTLVGVS H TNEEVRNM AEEFEYDDEP DEQGNPKKRP GKLSDYIPGP YPNEQAARAA ...String:
MFSNLSKRWA QRTLSKSFYS TATGAASKSG KLTQKLVTAG VAAAGITAST LLYADSLTAE AMTAAEHGL HAPAYAWSHN GPFETFDHAS IRRGYQVYRE VCAACHSLDR VAWRTLVGVS H TNEEVRNM AEEFEYDDEP DEQGNPKKRP GKLSDYIPGP YPNEQAARAA NQGALPPDLS LI VKARHGG CDYIFSLLTG YPDEPPAGVA LPPGSNYNPY FPGGSIAMAR VLFDDMVEYE DGT PATTSQ MAKDVTTFLN WCAEPEHDER KRLGLKTVII LSSLYLLSIW VKKFKWAGIK TRKF VFNPP KPRK

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Macromolecule #19: CYTOCHROME b-c1 COMPLEX SUBUNIT RIESKE

MacromoleculeName: CYTOCHROME b-c1 COMPLEX SUBUNIT RIESKE / type: protein_or_peptide / ID: 19 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MLGIRSSVKT CFKPMSLTSK RLISQSLLAS KSTYRTPNFD DVLKENNDAD KGRSYAYFMV GAMGLLSSA GAKSTVETFI SSMTATADVL AMAKVEVNLA AIPLGKNVVV KWQGKPVFIR H RTPHEIQE ANSVDMSALK DPQTDADRVK DPQWLIMLGI CTHLGCVPIG ...String:
MLGIRSSVKT CFKPMSLTSK RLISQSLLAS KSTYRTPNFD DVLKENNDAD KGRSYAYFMV GAMGLLSSA GAKSTVETFI SSMTATADVL AMAKVEVNLA AIPLGKNVVV KWQGKPVFIR H RTPHEIQE ANSVDMSALK DPQTDADRVK DPQWLIMLGI CTHLGCVPIG EAGDFGGWFC PC HGSHYDI SGRIRKGPAP LNLEIPAYEF DGDKVIVG

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Macromolecule #20: CYTOCHROME b-c1 COMPLEX SUBUNIT 6

MacromoleculeName: CYTOCHROME b-c1 COMPLEX SUBUNIT 6 / type: protein_or_peptide / ID: 20 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MLGIRSSVKT CFKPMSLTSK RLISQSLLAS KSTYRTPNFD DVLKENNDAD KGRSYAYFMV GAMGLLSSA GAKSTVETFI SSMTATADVL AMAKVEVNLA AIPLGKNVVV KWQGKPVFIR H RTPHEIQE ANSVDMSALK DPQTDADRVK DPQWLIMLGI CTHLGCVPIG ...String:
MLGIRSSVKT CFKPMSLTSK RLISQSLLAS KSTYRTPNFD DVLKENNDAD KGRSYAYFMV GAMGLLSSA GAKSTVETFI SSMTATADVL AMAKVEVNLA AIPLGKNVVV KWQGKPVFIR H RTPHEIQE ANSVDMSALK DPQTDADRVK DPQWLIMLGI CTHLGCVPIG EAGDFGGWFC PC HGSHYDI SGRIRKGPAP LNLEIPAYEF DGDKVIVG

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Macromolecule #21: CYTOCHROME b-c1 COMPLEX SUBUNIT 7

MacromoleculeName: CYTOCHROME b-c1 COMPLEX SUBUNIT 7 / type: protein_or_peptide / ID: 21 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MPQSFTSIAR IGDYILKSPV LSKLCVPVAN QFINLAGYKK LGLKFDDLIA EENPIMQTAL RRLPEDESY ARAYRIIRAH QTELTHHLLP RNEWIKAQED VPYLLPYILE AEAAAKEKDE L DNIEVSK

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Macromolecule #22: CYTOCHROME b-c1 COMPLEX SUBUNIT 8

MacromoleculeName: CYTOCHROME b-c1 COMPLEX SUBUNIT 8 / type: protein_or_peptide / ID: 22 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MGPPSGKTYM GWWGHMGGPK QKGITSYAVS PYAQKPLQGI FHNAVFNSFR RFKSQFLYVL IPAGIYWYW WKNGNEYNEF LYSKAGREEL ERVNV

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Macromolecule #23: CYTOCHROME b-c1 COMPLEX SUBUNIT 9

MacromoleculeName: CYTOCHROME b-c1 COMPLEX SUBUNIT 9 / type: protein_or_peptide / ID: 23 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MSFSSLYKTF FKRNAVFVGT IFAGAFVFQT VFDTAITSWY ENHNKGKLWK DVKARIAAGD GDDDDE

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Macromolecule #24: CYTOCHROME b-c1 COMPLEX SUBUNIT 10

MacromoleculeName: CYTOCHROME b-c1 COMPLEX SUBUNIT 10 / type: protein_or_peptide / ID: 24 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MAYTSHLSSK TGLHFGRLSL RSLTAYAPNL MLWGGASMLG LFVFTEGWPK FQDTLYKKIP LLGPTLEDH TPPEDKPN

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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: 7.2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details: 3 microliter of sample applied to negatively glow discharged grid, blot force -10; blotting time 8.5 sec..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.4 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

CTF correctionSoftware - Name: cryoSPARC (ver. 2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 65999
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2)
FSC plot (resolution estimation)

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