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- EMDB-10375: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex... -

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Basic information

Entry
Database: EMDB / ID: EMD-10375
TitleComplex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
Map dataThe reprocessed CIVa map after focused refinement with a mask including rcf2
Sample
  • Complex: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
    • Complex: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
      • Protein or peptide: x 12 types
    • Complex: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
      • Protein or peptide: x 1 types
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 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
DepositionOct 13, 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: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10375.png

Downloads & links

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Map

FileDownload / File: emd_10375.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe reprocessed CIVa map after focused refinement with a mask including rcf2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 536.576 Å		1.05 Å/pix.
x 512 pix.
= 536.576 Å		1.05 Å/pix.
x 512 pix.
= 536.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46 / Movie #1: 1
Minimum - Maximum-2.1611605 - 4.423754
Average (Standard dev.)0.0023443839 (±0.11214336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 536.576 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z536.576536.576536.576
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-2.1614.4240.002

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Supplemental data

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Sample components

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Entire : Complex IV in the III2-IV2 mitochondrial respiratory supercomplex...

EntireName: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
Components
  • Complex: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
    • Complex: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 1; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE I, COX1
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 2; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE II, COX2
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 4, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE IV, COX4
      • Protein or peptide: CYTOCHROME C OXIDASE POLYPEPTIDE 5A, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VA, COX5A
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 6, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VI, COX6
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7
      • Protein or peptide: CYTOCHROME C OXIDASE POLYPEPTIDE VIII, MITOCHONDRIAL; SYNONYM: COX8
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 6B; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIB, COX12
      • Protein or peptide: COX26; SYNONYM: Uncharacterized protein YDR119W-A
      • Protein or peptide: RCF2; SYNONYM: Respiratory supercomplex factor 2
    • Complex: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 6A, MITOCHONDRIAL; CYTOCHROME C OXIDASE POLYPEPTIDE VIA, COX13

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Supramolecule #1: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex...

SupramoleculeName: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: 13-subunit cytochrome c oxidase with isoform Cox5A

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Supramolecule #2: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex...

SupramoleculeName: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10, #12-#13 / Details: 13-subunit cytochrome c oxidase with isoform Cox5A
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Supramolecule #3: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex...

SupramoleculeName: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5A)-a)
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11 / Details: 13-subunit cytochrome c oxidase with isoform Cox5A
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: CYTOCHROME C OXIDASE SUBUNIT 1; SYNONYM: CYTOCHROME C OXIDASE POL...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 1; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE I, COX1
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 #2: CYTOCHROME C OXIDASE SUBUNIT 2; SYNONYM: CYTOCHROME C OXIDASE POL...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 2; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE II, COX2
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: DVPTPYACYF QDSATPNQEG ILELHDNIMF YLLVILGLVS WMLYT IVMT YSKNPIAYKY IKHGQTIEVI WTIFPAVILL IIAFPSFILL YLCDEVISPA MTIKAI GYQ WYWKYEYSDF INDSGETVEF ESYVIPDELL EEGQLRLLDT DTSMVVPVDT HIRFVVT AA ...String:
DVPTPYACYF QDSATPNQEG ILELHDNIMF YLLVILGLVS WMLYT IVMT YSKNPIAYKY IKHGQTIEVI WTIFPAVILL IIAFPSFILL YLCDEVISPA MTIKAI GYQ WYWKYEYSDF INDSGETVEF ESYVIPDELL EEGQLRLLDT DTSMVVPVDT HIRFVVT AA DVIHDFAIPS LGIKVDATPG RLNQVSALIQ REGVFYGACS ELCGTGHANM PIKIEAVS L PKFLEWLNEQ

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Macromolecule #3: CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POL...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3
type: protein_or_peptide / ID: 3 / 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 #4: CYTOCHROME C OXIDASE SUBUNIT 4, MITOCHONDRIAL; SYNONYM: CYTOCHROM...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 4, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE IV, COX4
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
QQKPVVKTAQ NLAEVNGPET LIGPGAKEGT VPTDL DQET GLARLELLGK LEGIDVFDTK PLDSSRKGTM KDPIIIESYD DYRYVGCTGS PAGSHT IMW LKPTVNEVAR CWECGSVYKL NPVGVPNDDH HH

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Macromolecule #5: CYTOCHROME C OXIDASE POLYPEPTIDE 5A, MITOCHONDRIAL; SYNONYM: CYTO...

MacromoleculeName: CYTOCHROME C OXIDASE POLYPEPTIDE 5A, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VA, COX5A
type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MLRNTFTRAG GLSRITSVRF AQTHALSNAA VMDLQSRWEN MPSTEQQDIV SKLSERQKLP WAQLTEPEK QAVWYISYGE WGPRRPVLNK GDSSFIAKGV AAGLLFSVGL FAVVRMAGGQ D AKTMNKEW QLKSDEYLKS KNANPWGGYS QVQSK

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Macromolecule #6: CYTOCHROME C OXIDASE SUBUNIT 6, MITOCHONDRIAL; SYNONYM: CYTOCHROM...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 6, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VI, COX6
type: protein_or_peptide / ID: 6 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
SDAHDEETFE EFTARYEKEF DEAYDLFEV QRVLNNCFSY DLVPAPAVIE KALRAARRVN DLPTAIRVFE ALKYKVENED Q YKAYLDEL KDVRQELGVP LKEELFPSSS

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Macromolecule #7: CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POL...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7
type: protein_or_peptide / ID: 7 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
ANKVIQLQKI FQSSTKPLWW RHPRSALYLY PFYAIFAVAV VTPLLYIPNA IRGIKAKKA

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Macromolecule #8: CYTOCHROME C OXIDASE POLYPEPTIDE VIII, MITOCHONDRIAL; SYNONYM: COX8

MacromoleculeName: CYTOCHROME C OXIDASE POLYPEPTIDE VIII, MITOCHONDRIAL; SYNONYM: COX8
type: protein_or_peptide / ID: 8 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MLCQQMIRTT AKRSSNIMTR PIIMKRSVHF KDGVYENIPF KVKGRKTPYA LSHFGFFAIG FAVPFVACYV QLKKSGAF

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Macromolecule #9: CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE PO...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9
type: protein_or_peptide / ID: 9 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
TIAPITGTIK RRVIMDIVLG FSLGGVMASY WWWGFHMDKI NKREKFYAEL AERKK

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Macromolecule #10: CYTOCHROME C OXIDASE SUBUNIT 6B; SYNONYM: CYTOCHROME C OXIDASE PO...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 6B; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIB, COX12
type: protein_or_peptide / ID: 10 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
DQENSPLHTV GFDARFPQQN QTKHCWQSYV DYHKCVNMKG EDFAPCKVFW KTYNALCP L DWIEKWDDQR EKGIFAGDIN SD

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Macromolecule #11: CYTOCHROME C OXIDASE SUBUNIT 6A, MITOCHONDRIAL; CYTOCHROME C OXID...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 6A, MITOCHONDRIAL; CYTOCHROME C OXIDASE POLYPEPTIDE VIA, COX13
type: protein_or_peptide / ID: 11 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
ASSLPPNALK PAFGPPDKVA AQKFKESLMA TEKHAKDTSN MWVKISVWVA L PAIALTAV NTYFVEKEHA EHREHLKHVP DSEWPRDYEF MNIRSKPFFW GDGDKTLFWN PV VNRHIEH DDG ARGSHH HHHH

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Macromolecule #12: COX26; SYNONYM: Uncharacterized protein YDR119W-A

MacromoleculeName: COX26; SYNONYM: Uncharacterized protein YDR119W-A / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MFFSQVLRSS ARAAPIKRYT GGRIGESWVI TEGRRLIPEI FQWSAVLSVC LGWPGAVYFF SKARKA

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Macromolecule #13: RCF2; SYNONYM: Respiratory supercomplex factor 2

MacromoleculeName: RCF2; SYNONYM: Respiratory supercomplex factor 2 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
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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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 uL 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) / Number real images: 2740 / Average electron dose: 52.64 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: CTFFIND (ver. 4) / Software - details: within cryosparc 2
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6t15

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 44194
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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