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- EMDB-53029: CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II -

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Basic information

Entry
Database: EMDB / ID: EMD-53029
TitleCRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II
Map datayeast Complex II with UQ6
Sample
  • Complex: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4
    • Protein or peptide: x 4 types
  • Ligand: x 9 types
KeywordsCOMPLEX II / MEMBRANE PROTEIN / OXIDOREDUCTASE / UBIQUINONE-1
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / TIM22 mitochondrial import inner membrane insertion complex / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / cellular respiration / 3 iron, 4 sulfur cluster binding ...Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / TIM22 mitochondrial import inner membrane insertion complex / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / cellular respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding / quinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit ...Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 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
Similarity search - Domain/homology
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsPinotsis N / Marechal A / Berry EA / Shu C
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T032154/1 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Commun Biol / Year: 2026
Title: Cryo-EM structure of bixafen-bound S. cerevisiae complex II unravels SDHI specificity against pathogenic fungi.
Authors: Nikos Pinotsis / Claudia Burn-Leefe / Sarah Jones / Shu Chen / Natalya Lukoyanova / Brigitte Meunier / Edward A Berry / Amandine Maréchal /
Abstract: Respiratory complex II (CII), or succinate dehydrogenase, couples succinate oxidation in the Krebs cycle with electron transfer to the respiratory chain. Owing to this pivotal role, CII inhibitors ...Respiratory complex II (CII), or succinate dehydrogenase, couples succinate oxidation in the Krebs cycle with electron transfer to the respiratory chain. Owing to this pivotal role, CII inhibitors are widely used fungicides globally; however, their development has largely proceeded without structural insights from fungal targets. Here, we report cryo-electron microscopy structures of the 128 kDa mitochondrial CII from Saccharomyces cerevisiae in two states: active, with endogenous ubiquinone-6 bound (3.15 Å), and inhibited with the fungicide bixafen (3.00 Å). Although closely related to the mammalian type C enzyme, our structures show that the yeast CII has lost the canonical heme cofactor. They also reveal how clade-specific sequence extensions of the membrane subunits Sdh3 and Sdh4 - conserved in pathogenic fungi - uniquely contribute to complex stability and fungicide binding. Our findings provide a foundation for rational design of next-generation CII inhibitors and combatting resistance, in both agriculture and human health.
History
DepositionMar 6, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53029.png

Downloads & links

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Map

FileDownload / File: emd_53029.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationyeast Complex II with UQ6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 340 pix.
= 281.52 Å		0.83 Å/pix.
x 340 pix.
= 281.52 Å		0.83 Å/pix.
x 340 pix.
= 281.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.6727359 - 1.6256435
Average (Standard dev.)-0.00007606046 (±0.02381417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 281.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B, yeast Complex II with UQ6

Fileemd_53029_half_map_1.map
AnnotationHalf map B, yeast Complex II with UQ6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A, yeast Complex II with UQ6

Fileemd_53029_half_map_2.map
AnnotationHalf map A, yeast Complex II with UQ6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 ...

EntireName: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4
Components
  • Complex: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: POTASSIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: Ubiquinone-6
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: hexacosanoic acid
  • Ligand: water

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Supramolecule #1: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 ...

SupramoleculeName: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 128 KDa

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Macromolecule #1: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitoch...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 70.404453 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLSLKKSALS KLTLLRNTRT FTSSALVRQT QGSVNGSASR SADGKYHIID HEYDCVVIGA GGAGLRAAFG LAEAGYKTAC ISKLFPTRS HTVAAQGGIN AALGNMHKDN WKWHMYDTVK GSDWLGDQDS IHYMTREAPK SIIELEHYGV PFSRTENGKI Y QRAFGGQT ...String:
MLSLKKSALS KLTLLRNTRT FTSSALVRQT QGSVNGSASR SADGKYHIID HEYDCVVIGA GGAGLRAAFG LAEAGYKTAC ISKLFPTRS HTVAAQGGIN AALGNMHKDN WKWHMYDTVK GSDWLGDQDS IHYMTREAPK SIIELEHYGV PFSRTENGKI Y QRAFGGQT KEYGKGAQAY RTCAVADRTG HALLHTLYGQ ALRHDTHFFI EYFALDLLTH NGEVVGVIAY NQEDGTIHRF RA HKTIIAT GGYGRAYFSC TSAHT(CME)TGDG NAMVSRAGFP LQDLEFVQFH PSGIYGSGCL ITEGARGEGG FLVNSEGER FMERYAPTAK DLACRDVVSR AITMEIREGR GVGKKKDHMY LQLSHLPPEV LKERLPGISE TAAIFAGVDV TKEPIPIIPT VHYNMGGIP TKWNGEALTI DEETGEDKVI PGLMACGEAA CVSVHGANRL GANSLLDLVV FGRAVAHTVA DTLQPGLPHK P LPSDLGKE SIANLDKLRN ANGSRSTAEI RMNMKQTMQK DVSVFRTQSS LDEGVRNITA VEKTFDDVKT TDRSMIWNSD LV ETLELQN LLTCASQTAV SAANRKESRG AHAREDYPNR DDEHWMKHTL SWQKDVAAPV TLKYRRVIDH TLDEKECPSV PPT VRAY

UniProtKB: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

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Macromolecule #2: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitocho...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.34741 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLNVLLRRKA FCLVTKKGMA TATTAAATHT PRLKTFKVYR WNPDEPSAKP HLQSYQVDLN DCGPMVLDAL LKIKDEQDST LTFRRSCRE GICGSCAMNI GGRNTLACI(CME) KIDQNESKQL KIYPLPHMFI VKDLVPDLTN FYQQYKSIQP YLQRSSF PK DGTEVLQSIE ...String:
MLNVLLRRKA FCLVTKKGMA TATTAAATHT PRLKTFKVYR WNPDEPSAKP HLQSYQVDLN DCGPMVLDAL LKIKDEQDST LTFRRSCRE GICGSCAMNI GGRNTLACI(CME) KIDQNESKQL KIYPLPHMFI VKDLVPDLTN FYQQYKSIQP YLQRSSF PK DGTEVLQSIE DRKKLDGLYE CILCACCSTS CPSYWWNQEQ YLGPAVLMQA YRWLIDSRDQ ATKTRKAMLN NSMSLYRC H TIMNCTRTCP KGLNPGLAIA EIKKSLAFA

UniProtKB: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

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Macromolecule #3: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitoch...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
type: protein_or_peptide / ID: 3
Details: The specific variant has the following modifications compared to P33421: Ser14Pro Lys74Arg Leu95Phe
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508/S288c
Molecular weightTheoretical: 22.167031 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MSAMMVKLGL NKPALLLKPS AFSRAAALSS SRRLLFNTAR TNFLSTSPLK NVASEMNTKA AIAEEQILNK QRARRPISPH LTIYQPQLT WYLSSFHRIS LVLMGLGFYL FTILFGVSGL LGLGLTTEKV SNWYHQKFSK ITEWSIKGSF AYLFAIHYGG A IRHLIWDT ...String:
MSAMMVKLGL NKPALLLKPS AFSRAAALSS SRRLLFNTAR TNFLSTSPLK NVASEMNTKA AIAEEQILNK QRARRPISPH LTIYQPQLT WYLSSFHRIS LVLMGLGFYL FTILFGVSGL LGLGLTTEKV SNWYHQKFSK ITEWSIKGSF AYLFAIHYGG A IRHLIWDT AKELTLKGVY RTGYALIGFT AVLGTYLLTL

UniProtKB: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial

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Macromolecule #4: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, ...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
type: protein_or_peptide / ID: 4 / Details: Modified with an N-terminal His-Tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508/S288c
Molecular weightTheoretical: 22.081473 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MMLPRSMKFM TGRRIFHTAT VRAFQSTAKK SLTIPFLPVL PQKPGGVRGT PNDAYVPPPE NKLEGSYHWY MEKIFALSVV PLATTAMLT TGPLSTAADS FFSVMLLGYC YMEFNSCITD YISERVYGVW HKYAMYMLGL GSAVSLFGIY KLETENDGVV G LVKSLWDS ...String:
MMLPRSMKFM TGRRIFHTAT VRAFQSTAKK SLTIPFLPVL PQKPGGVRGT PNDAYVPPPE NKLEGSYHWY MEKIFALSVV PLATTAMLT TGPLSTAADS FFSVMLLGYC YMEFNSCITD YISERVYGVW HKYAMYMLGL GSAVSLFGIY KLETENDGVV G LVKSLWDS SEKDNSQKIE AKKGARGSHH HHHHHHHH

UniProtKB: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

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Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / 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 #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 7 / 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 #8: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #9: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #10: Ubiquinone-6

MacromoleculeName: Ubiquinone-6 / type: ligand / ID: 10 / Number of copies: 1 / Formula: A1J2J
Molecular weightTheoretical: 590.875 Da

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Macromolecule #11: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 11 / Number of copies: 1 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

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Macromolecule #12: hexacosanoic acid

MacromoleculeName: hexacosanoic acid / type: ligand / ID: 12 / Number of copies: 1 / Formula: 7PO
Molecular weightTheoretical: 396.69 Da
Chemical component information

ChemComp-7PO:
hexacosanoic acid

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 18 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.025 mg/mL
BufferpH: 7.2 / Component - Concentration: 50.0 mM / Component - Name: HEPES / Details: 150 mM NaCl 0.05% GDN
GridModel: C-flat-1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 20000 / Average exposure time: 2.5 sec. / Average electron dose: 18.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 149808
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

0711

source_name: AlphaFold, initial_model_type: in silico model

1801

source_name: AlphaFold, initial_model_type: in silico model

3421

source_name: AlphaFold, initial_model_type: in silico model

7298

source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qdl:
CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II

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