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- EMDB-15866: Cryo-EM structure of succinate dehydrogenase complex (complex-II)... -

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Basic information

Entry
Database: EMDB / ID: EMD-15866
TitleCryo-EM structure of succinate dehydrogenase complex (complex-II) in respiratory supercomplex of Tetrahymena thermophila
Map dataSharpened mask refined map
Sample
  • Complex: Succinate dehydrogenase complex (complex-II)
    • Protein or peptide: x 15 types
  • Ligand: x 10 types
KeywordsCiliate / Mitochondrial / Complex-II / Supercomplex / ELECTRON TRANSPORT
Function / homology
Function and homology information


mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / membrane
Similarity search - Function
Succinate dehydrogenase, flavoprotein subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain ...Succinate dehydrogenase, flavoprotein subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Diphthamide synthesis protein / succinate dehydrogenase / Uncharacterized protein / Transmembrane protein, putative / Uncharacterized protein / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Transmembrane protein / Transmembrane protein, putative / Transmembrane protein, putative / Transmembrane protein, putative ...Diphthamide synthesis protein / succinate dehydrogenase / Uncharacterized protein / Transmembrane protein, putative / Uncharacterized protein / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Transmembrane protein / Transmembrane protein, putative / Transmembrane protein, putative / Transmembrane protein, putative / NmrA-like domain-containing protein / Uncharacterized protein / Transmembrane protein, putative
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMuhleip A / Kock Flygaard R / Baradaran R / Amunts A
Funding support Sweden, European Union, 4 items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
Cancerfonden2017/1041 Sweden
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
Citation
Journal: Nature / Year: 2023
Title: Structural basis of mitochondrial membrane bending by the I-II-III-IV supercomplex.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Rozbeh Baradaran / Outi Haapanen / Thomas Gruhl / Victor Tobiasson / Amandine Maréchal / Vivek Sharma / Alexey Amunts /
Abstract: Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes ...Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III-IV supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex
Authors: Muhleip A / Flygaard RK / Haapanen O / Baradaran R / Gruhl T / Tobiasson V / Marechal A / Sharma V / Amunts A
History
DepositionSep 27, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15866.png

Downloads & links

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Map

FileDownload / File: emd_15866.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened mask refined map
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 480 pix.
= 600. Å		1.25 Å/pix.
x 480 pix.
= 600. Å		1.25 Å/pix.
x 480 pix.
= 600. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.2404299 - 6.277895
Average (Standard dev.)-0.0035404132 (±0.10862157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 600.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15866_msk_1.map
Projections & Slices
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Slices (1/2)
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Histogram

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Additional map: Unsharpened mask refined map

Fileemd_15866_additional_1.map
AnnotationUnsharpened mask refined map
Projections & Slices
AxesZYX

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Half map: Half-map A

Fileemd_15866_half_map_1.map
AnnotationHalf-map A
Projections & Slices
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Half map: Half-map B

Fileemd_15866_half_map_2.map
AnnotationHalf-map B
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Sample components

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Entire : Succinate dehydrogenase complex (complex-II)

EntireName: Succinate dehydrogenase complex (complex-II)
Components
  • Complex: Succinate dehydrogenase complex (complex-II)
    • Protein or peptide: Diphthamide synthesis protein
    • Protein or peptide: Transmembrane protein, putative
    • Protein or peptide: Transposase
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
    • Protein or peptide: DUF4885 domain-containing protein
    • Protein or peptide: Succinate dehydrogenase (quinone)
    • Protein or peptide: Transmembrane protein, putative
    • Protein or peptide: SDHTT3
    • Protein or peptide: Transmembrane protein, putative
    • Protein or peptide: NmrA domain-containing protein
    • Protein or peptide: Transmembrane protein, putative
    • Protein or peptide: Transmembrane protein, putative
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: SDHTT11
    • Protein or peptide: SDHD
  • Ligand: CARDIOLIPIN
  • Ligand: CALCIUM ION
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: HEME C
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: Ubiquinone-8

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Supramolecule #1: Succinate dehydrogenase complex (complex-II)

SupramoleculeName: Succinate dehydrogenase complex (complex-II) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Details: Complex-II of the mitochondrial respiratory chain in Tetrahymena thermophila
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Organelle: Mitochondrion
Molecular weightTheoretical: 305 KDa

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Macromolecule #1: Diphthamide synthesis protein

MacromoleculeName: Diphthamide synthesis protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 22.894336 KDa
SequenceString: MLTQRFYMIQ FTKEEQSSEE KYLKTREREE DRKKELMHPQ KVLNKKENKR KALLSKNQQN KKLIKYLNLN KRQEKLININ QEEMSILPP LQYTYSNEES LELLIHSIKG NKDCNSERKA FNLCRSTVLG KHVEPEKCLD KALVFVNCFQ KVRRDESAAC Q SAFNSTLE ...String:
MLTQRFYMIQ FTKEEQSSEE KYLKTREREE DRKKELMHPQ KVLNKKENKR KALLSKNQQN KKLIKYLNLN KRQEKLININ QEEMSILPP LQYTYSNEES LELLIHSIKG NKDCNSERKA FNLCRSTVLG KHVEPEKCLD KALVFVNCFQ KVRRDESAAC Q SAFNSTLE CGKKYSESTI SLGSSCQSQL DAYLNCK

UniProtKB: Diphthamide synthesis protein

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Macromolecule #2: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 9.168366 KDa
SequenceString:
MARLWWTLDP SKYYLKQISS GGRNEILFTV LGVTAAYWYF GNKRCEHYWR RQIDNCQSWS RAQNINGNNL TVKQYF

UniProtKB: Transmembrane protein, putative

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Macromolecule #3: Transposase

MacromoleculeName: Transposase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 11.027419 KDa
SequenceString:
MKLDQIISYY ITPVRRFDKN LTAEQIYEQY QQAAQFNEID AFTNIRFHRK FKEYIQTQEQ SDYLYEKAKQ ISTLAQKMFE KKFPEYYTQ

UniProtKB: Uncharacterized protein

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Macromolecule #4: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitoch...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 70.082758 KDa
SequenceString: MFKYLSKIQR VTLHSKVSKN FAVLSKDHPE KGPSQGHLTD KYTVIDHTYD AIVVGAGGAG LRAAFGLVEE GFKTACITKL FPTRSHTVA AQGGINAALG NMTEDDWKWH FYDTVKGSDW LGDQDAIQYM TREAPAAVLE LESYGLPFSR TPEGKIYQRA F GGQSLKFG ...String:
MFKYLSKIQR VTLHSKVSKN FAVLSKDHPE KGPSQGHLTD KYTVIDHTYD AIVVGAGGAG LRAAFGLVEE GFKTACITKL FPTRSHTVA AQGGINAALG NMTEDDWKWH FYDTVKGSDW LGDQDAIQYM TREAPAAVLE LESYGLPFSR TPEGKIYQRA F GGQSLKFG KGGQARRTAC AADRTGHAML HTLFGRSLAY NCNFFIEYFV IDLIMDEEGA CRGVICMSMA DGSIHRIRAH YT VLAAGGY GRSYLSCTAA HTCTGDGMAL ATRAGLPLED PEFVQFHPTG IYGSGCLMTE GCRGEGGILV NSNGEAFMEK YAP TAKDLA SRDVVSRAMT IEILEGRGVG PKKDHIFLQL HHLSPETLHQ RLPGISETAR IFAGVDVTKE PAPVVPTVHY NMGG VPTNW KTEVITQDKN GKDKIVPGLL AAGENACASV HGANRLGANS LLDIVVFGRA AAKLVKEKLK PGTPHKDLPK NAGEQ ALAR LDKYRFANGE YTTHHVRTAM QETMQRHAAV FRIEKLMAEG VQKLDHIYEQ SKSLKTFDRG LVWNTDLIET LELENL LLC SKQTLLAGLL RKESRGAHAR DDFKERDDKN WMKHSLTWIK DVNTGKTEVT YRDVINHTLD SEVTPVPPAK RSY

UniProtKB: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

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Macromolecule #5: DUF4885 domain-containing protein

MacromoleculeName: DUF4885 domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 12.979428 KDa
SequenceString:
MFSDFNMYEA KVFLKAVADA QNTFRQTAQQ ENQLARYESQ SQSLLNGSTS GAISITGDNI QQGRNFKALK EVKLFQYSNE IFKKYLAGF DSFSGDYTAF KKFLNESVKK IEQDA

UniProtKB: Uncharacterized protein

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Macromolecule #6: Succinate dehydrogenase (quinone)

MacromoleculeName: Succinate dehydrogenase (quinone) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 36.002402 KDa
SequenceString: MLRTIFKTRS LFNASVSRFG SGFDRIAESN DATSICLESI SGTIKGLQKA NYVVEHNPNL TSEEKKHLKQ FLVYRYNPAD PHDQPKYVS YWCDIKKFPP MFLDAILYIK NELDPTLSIR RSCREGICGS CAVNCDGLHT LACISGFNRD LSKPTIITPL G HMFILKDL ...String:
MLRTIFKTRS LFNASVSRFG SGFDRIAESN DATSICLESI SGTIKGLQKA NYVVEHNPNL TSEEKKHLKQ FLVYRYNPAD PHDQPKYVS YWCDIKKFPP MFLDAILYIK NELDPTLSIR RSCREGICGS CAVNCDGLHT LACISGFNRD LSKPTIITPL G HMFILKDL VVDMTNFYAQ YKMIEPYLKR KTPKPDANKE YPQSPEQRAL LDGLYECVLC AACSTSCPSY WWHPDRYLGP AI LQQAYRW IVDSRDEYTQ ERIERIAEDV RLDDCQQIGM CSFTCPKGLN PQLSLKNLMD MVKDFRQKRI EQEVL

UniProtKB: succinate dehydrogenase

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Macromolecule #7: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 35.124293 KDa
SequenceString: MIKYLLHQLF IYIYVAEVLL GCIFAFAETV FFHSDQDEDY FLQIKQIQIK NQKRFRNNQK KSRSFKKKII NQQLVSKMVR LNLKSNVDQ NEYPFLAKWD KDMRQNYEEY QNRIDATTYH LQRSQRGIAV FGEWMYPRYF QKDILELEVL RRKQQLGKIY P EEVSSYTQ ...String:
MIKYLLHQLF IYIYVAEVLL GCIFAFAETV FFHSDQDEDY FLQIKQIQIK NQKRFRNNQK KSRSFKKKII NQQLVSKMVR LNLKSNVDQ NEYPFLAKWD KDMRQNYEEY QNRIDATTYH LQRSQRGIAV FGEWMYPRYF QKDILELEVL RRKQQLGKIY P EEVSSYTQ INPDIANDLN LTFNAKLLWP VRGMTVGAGF FAFAHLFNLP YSFRLGLFVL PTAVELAFTW GNKTSQFKSI EF MDYLLQY RVSKALLEKN AKHFAEKKAA YQKEINSSQS VQDLYNQLIT LVSEQAPSE

UniProtKB: Transmembrane protein, putative

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Macromolecule #8: SDHTT3

MacromoleculeName: SDHTT3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 23.62773 KDa
SequenceString: MSLVSLFKNT FLKSRVIGLS FQAQRVMAQM AKTDFENPDE HFLLNDAMKY NELVFYGRLA ENWSINPELF GKAELAKYNE AKQTLIDFN QYHALVQNLH EFYWELKTIY LELSRGVATS NFHNKREVTH SIIESDIKNS IHKYIQLIDD LKDYPEWQHK V REEIGYYA ...String:
MSLVSLFKNT FLKSRVIGLS FQAQRVMAQM AKTDFENPDE HFLLNDAMKY NELVFYGRLA ENWSINPELF GKAELAKYNE AKQTLIDFN QYHALVQNLH EFYWELKTIY LELSRGVATS NFHNKREVTH SIIESDIKNS IHKYIQLIDD LKDYPEWQHK V REEIGYYA HMIYTSVNHD GNFPEIFKEF NKVDSLYYFK

UniProtKB: Uncharacterized protein

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Macromolecule #9: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 11.188824 KDa
SequenceString:
MLDDTKYIQM AQKFPRNVSV QLNKKLFVTR TWFRNYYFVG VFGIFAYFIY NQPKIFAPFS GYPTTVAYKA QPDFLNDQVI FYSQQRQNT LKNF

UniProtKB: Transmembrane protein, putative

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Macromolecule #10: NmrA domain-containing protein

MacromoleculeName: NmrA domain-containing protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 36.376008 KDa
SequenceString: MSLLVVSGAN KVGQGIIRGL HSSGKYEKIV VADVFPKYYY LERYLRFKDT LTQNKTKLEE VKLTDKTDLE SAIKKASHVV YVTHDYYYN VPSKLNLIKH TATLSRSAGV KRLVNVTPVE NDHYGESQAV LAATQSENEA RVAFPGLVEL KTDLTFGQDS T VVSELLTR ...String:
MSLLVVSGAN KVGQGIIRGL HSSGKYEKIV VADVFPKYYY LERYLRFKDT LTQNKTKLEE VKLTDKTDLE SAIKKASHVV YVTHDYYYN VPSKLNLIKH TATLSRSAGV KRLVNVTPVE NDHYGESQAV LAATQSENEA RVAFPGLVEL KTDLTFGQDS T VVSELLTR LAYGKSIYFK PSAHRISPVH TLNVAEATQR ILENNSLQNL RYVARGTESF DWNTIISTLA AAIGKNANLN QN PLENIIS PLSDNIVSQT VHHHHYLNLT RFINQYQEPK QTEHHELTNL GVNNLVKFSE FYKPNSVSTQ DYQIKTGLSH WAH CL

UniProtKB: NmrA-like domain-containing protein

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Macromolecule #11: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 11.957518 KDa
SequenceString:
MNHSCQKVFE GFVSALYDTS YFFRNFGPFK ATIHYATYAN YLAQNWAPRV SYIETSTPAY TLAKNKYAVY IVYGLIGGAL IHNYMLDNK AAQKSQQYYL KHRD

UniProtKB: Transmembrane protein, putative

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Macromolecule #12: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 7.244434 KDa
SequenceString:
MRRIFWNFKT AFVGLPMFSL APKNILVYPI VVGVPLYTFI VLQNSVRGFA YFDEYDSDVK EN

UniProtKB: Transmembrane protein, putative

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Macromolecule #13: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210
Molecular weightTheoretical: 7.03602 KDa
SequenceString:
MRTKLYNAAY FLLNNNESFG HSFGIRLKIV GLNTWIVGYA VSRYYFSSLR VKAAQDERFE

UniProtKB: Transmembrane protein

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Macromolecule #14: SDHTT11

MacromoleculeName: SDHTT11 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 5.158135 KDa
SequenceString:
LPIRNIQFAR YHYLAAVTVF TYFATRCCLL DYKKYYPLAS VKK

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Macromolecule #15: SDHD

MacromoleculeName: SDHD / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 5.566625 KDa
SequenceString:
MFKELIHIFR TYYITFRYLK KSNINFLKNL SYTLIAYYLI INFQ

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Macromolecule #16: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 16 / Number of copies: 7 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #17: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 17 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #18: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 18 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #19: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 19 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #20: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 20 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #21: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 21 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #22: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 22 / Number of copies: 3 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #23: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 23 / Number of copies: 1 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #24: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 24 / Number of copies: 1 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #25: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 25 / Number of copies: 1 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 25.66 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138746
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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