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- EMDB-10317: Complex III of the III2-IV(5B)1 respiratory supercomplex from S. ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10317
TitleComplex III of the III2-IV(5B)1 respiratory supercomplex from S. cerevisiae after focused refinement
Map dataNone
Sample
  • Complex: Complex III of the III2-IV(5B)1 respiratory supercomplex from S. cerevisiae after focused refinement
    • Protein or peptide: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
    • Protein or peptide: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
    • Protein or peptide: CYTOCHROME B
    • Protein or peptide: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
    • Protein or peptide: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
    • 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
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 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 18, 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: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10317.png

Downloads & links

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Map

FileDownload / File: emd_10317.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.048 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.7
Minimum - Maximum-1.5276842 - 3.2818265
Average (Standard dev.)0.010998556 (±0.09880309)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 402.432 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z402.432402.432402.432
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.5283.2820.011

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Supplemental data

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Sample components

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Entire : Complex III of the III2-IV(5B)1 respiratory supercomplex from S. ...

EntireName: Complex III of the III2-IV(5B)1 respiratory supercomplex from S. cerevisiae after focused refinement
Components
  • Complex: Complex III of the III2-IV(5B)1 respiratory supercomplex from S. cerevisiae after focused refinement
    • Protein or peptide: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
    • Protein or peptide: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
    • Protein or peptide: CYTOCHROME B
    • Protein or peptide: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
    • Protein or peptide: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
    • 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: Complex III of the III2-IV(5B)1 respiratory supercomplex from S. ...

SupramoleculeName: Complex III of the III2-IV(5B)1 respiratory supercomplex from S. cerevisiae after focused refinement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL

MacromoleculeName: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
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 #2: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL

MacromoleculeName: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
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 #3: CYTOCHROME B

MacromoleculeName: CYTOCHROME B / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
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 #4: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL

MacromoleculeName: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL / type: protein_or_peptide / ID: 4 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
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 #5: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL

MacromoleculeName: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL / type: protein_or_peptide / ID: 5 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
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 #6: CYTOCHROME B-C1 COMPLEX SUBUNIT 6

MacromoleculeName: CYTOCHROME B-C1 COMPLEX SUBUNIT 6 / type: protein_or_peptide / ID: 6 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
SequenceString:
MGMLELVGEY WEQLKITVVP VVAAAEDDDN EQHEEKAAEG EEKEEENGDE DEDEDEDEDD DDDDDEDEE EEEEVTDQLE DLREHFKNTE EGKALVHHYE ECAERVKIQQ QQPGYADLEH K EDCVEEFF HLQHYLDTAT APRLFDKLK

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Macromolecule #7: CYTOCHROME B-C1 COMPLEX SUBUNIT 7

MacromoleculeName: CYTOCHROME B-C1 COMPLEX SUBUNIT 7 / type: protein_or_peptide / ID: 7 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
SequenceString:
MPQSFTSIAR IGDYILKSPV LSKLCVPVAN QFINLAGYKK LGLKFDDLIA EENPIMQTAL RRLPEDESY ARAYRIIRAH QTELTHHLLP RNEWIKAQED VPYLLPYILE AEAAAKEKDE L DNIEVSK

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Macromolecule #8: CYTOCHROME B-C1 COMPLEX SUBUNIT 8

MacromoleculeName: CYTOCHROME B-C1 COMPLEX SUBUNIT 8 / type: protein_or_peptide / ID: 8 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
SequenceString:
MGPPSGKTYM GWWGHMGGPK QKGITSYAVS PYAQKPLQGI FHNAVFNSFR RFKSQFLYVL IPAGIYWYW WKNGNEYNEF LYSKAGREEL ERVNV

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Macromolecule #9: CYTOCHROME B-C1 COMPLEX SUBUNIT 9

MacromoleculeName: CYTOCHROME B-C1 COMPLEX SUBUNIT 9 / type: protein_or_peptide / ID: 9 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
SequenceString:
MSFSSLYKTF FKRNAVFVGT IFAGAFVFQT VFDTAITSWY ENHNKGKLWK DVKARIAAGD GDDDDE

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Macromolecule #10: CYTOCHROME B-C1 COMPLEX SUBUNIT 10

MacromoleculeName: CYTOCHROME B-C1 COMPLEX SUBUNIT 10 / type: protein_or_peptide / ID: 10 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288C
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 73042
FSC plot (resolution estimation)

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