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- EMDB-34225: cryo-EM structure of the human respiratory complex II -

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Basic information

Entry
Database: EMDB / ID: EMD-34225
Titlecryo-EM structure of the human respiratory complex II
Map data
Sample
  • Complex: The human mitochondrial complex II, composed of SDHA, SDHB, SDHC and SDHD
    • Protein or peptide: x 4 types
  • Ligand: x 7 types
Keywordssuccinate dehydrogenase / electron transport chain / human mitochondria / OXIDOREDUCTASE / oxidative phosphorylation
Function / homology
Function and homology information


regulation of catecholamine secretion / succinate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle ...regulation of catecholamine secretion / succinate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport / mitochondrial envelope / 3 iron, 4 sulfur cluster binding / ubiquinone binding / proton motive force-driven mitochondrial ATP synthesis / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / nervous system development / 4 iron, 4 sulfur cluster binding / cellular response to hypoxia / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / heme binding / nucleolus / mitochondrion / nucleoplasm / membrane / metal ion binding / plasma membrane
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 / Fumarate reductase/succinate dehydrogenase, transmembrane 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 / Fumarate reductase/succinate dehydrogenase, transmembrane 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 / Alpha-helical ferredoxin / FAD binding domain / 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] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsDu Z / Zhou X / Lai Y / Xu J / Zhang Y / Zhou S / Liu F / Gao Y / Gong H / Rao Z
Funding support China, 3 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020200 China
National Natural Science Foundation of China (NSFC)81520108019, 813300237,32100976,82222042 China
Chinese Academy of Sciences2017YFC0840300,2020YFA0707500 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure of the human respiratory complex II.
Authors: Zhanqiang Du / Xiaoting Zhou / Yuezheng Lai / Jinxu Xu / Yuying Zhang / Shan Zhou / Ziyan Feng / Long Yu / Yanting Tang / Weiwei Wang / Lu Yu / Changlin Tian / Ting Ran / Hongming Chen / ...Authors: Zhanqiang Du / Xiaoting Zhou / Yuezheng Lai / Jinxu Xu / Yuying Zhang / Shan Zhou / Ziyan Feng / Long Yu / Yanting Tang / Weiwei Wang / Lu Yu / Changlin Tian / Ting Ran / Hongming Chen / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong /
Abstract: Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been ...Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been shown to cause mitochondrial disease and some types of cancers. However, the structure of this complex is yet to be resolved, hindering a comprehensive understanding of the functional aspects of this molecular machine. Here, we have determined the structure of human complex II in the presence of ubiquinone at 2.86 Å resolution by cryoelectron microscopy, showing it comprises two water-soluble subunits, SDHA and SDHB, and two membrane-spanning subunits, SDHC and SDHD. This structure allows us to propose a route for electron transfer. In addition, clinically relevant mutations are mapped onto the structure. This mapping provides a molecular understanding to explain why these variants have the potential to produce disease.
History
DepositionSep 5, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34225.png

Downloads & links

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Map

FileDownload / File: emd_34225.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.1288904 - 1.6354086
Average (Standard dev.)0.00020459799 (±0.029110845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34225_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34225_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : The human mitochondrial complex II, composed of SDHA, SDHB, SDHC ...

EntireName: The human mitochondrial complex II, composed of SDHA, SDHB, SDHC and SDHD
Components
  • Complex: The human mitochondrial complex II, composed of SDHA, SDHB, SDHC and SDHD
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: UBIQUINONE-1
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: The human mitochondrial complex II, composed of SDHA, SDHB, SDHC ...

SupramoleculeName: The human mitochondrial complex II, composed of SDHA, SDHB, SDHC and SDHD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #4, #3, #2
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 72.786469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGVRGLSRL LSARRLALAK AWPTVLQTGT RGFHFTVDGN KRASAKVSDS ISAQYPVVDH EFDAVVVGAG GAGLRAAFGL SEAGFNTAC VTKLFPTRSH TVAAQGGINA ALGNMEEDNW RWHFYDTVKG SDWLGDQDAI HYMTEQAPAA VVELENYGMP F SRTEDGKI ...String:
MSGVRGLSRL LSARRLALAK AWPTVLQTGT RGFHFTVDGN KRASAKVSDS ISAQYPVVDH EFDAVVVGAG GAGLRAAFGL SEAGFNTAC VTKLFPTRSH TVAAQGGINA ALGNMEEDNW RWHFYDTVKG SDWLGDQDAI HYMTEQAPAA VVELENYGMP F SRTEDGKI YQRAFGGQSL KFGKGGQAHR CCCVADRTGH SLLHTLYGRS LRYDTSYFVE YFALDLLMEN GECRGVIALC IE DGSIHRI RAKNTVVATG GYGRTYFSCT SAHTSTGDGT AMITRAGLPC QDLEFVQFHP TGIYGAGCLI TEGCRGEGGI LIN SQGERF MERYAPVAKD LASRDVVSRS MTLEIREGRG CGPEKDHVYL QLHHLPPEQL ATRLPGISET AMIFAGVDVT KEPI PVLPT VHYNMGGIPT NYKGQVLRHV NGQDQIVPGL YACGEAACAS VHGANRLGAN SLLDLVVFGR ACALSIEESC RPGDK VPPI KPNAGEESVM NLDKLRFADG SIRTSELRLS MQKSMQNHAA VFRVGSVLQE GCGKISKLYG DLKHLKTFDR GMVWNT DLV ETLELQNLML CALQTIYGAE ARKESRGAHA REDYKVRIDE YDYSKPIQGQ QKKPFEEHWR KHTLSYVDVG TGKVTLE YR PVIDKTLNEA DCATVPPAIR SY

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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.674811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAVVALSLR RRLPATTLGG ACLQASRGAQ TAAATAPRIK KFAIYRWDPD KAGDKPHMQT YEVDLNKCGP MVLDALIKIK NEVDSTLTF RRSCREGICG SCAMNINGGN TLACTRRIDT NLNKVSKIYP LPHMYVIKDL VPDLSNFYAQ YKSIEPYLKK K DESQEGKQ ...String:
MAAVVALSLR RRLPATTLGG ACLQASRGAQ TAAATAPRIK KFAIYRWDPD KAGDKPHMQT YEVDLNKCGP MVLDALIKIK NEVDSTLTF RRSCREGICG SCAMNINGGN TLACTRRIDT NLNKVSKIYP LPHMYVIKDL VPDLSNFYAQ YKSIEPYLKK K DESQEGKQ QYLQSIEERE KLDGLYECIL CACCSTSCPS YWWNGDKYLG PAVLMQAYRW MIDSRDDFTE ERLAKLQDPF SL YRCHTIM NCTRTCPKGL NPGKAIAEIK KMMATYKEKK ASV

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

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Macromolecule #3: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial

MacromoleculeName: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.632213 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAALLLRHVG RHCLRAHFSP QLCIRNAVPL GTTAKEEMER FWNKNIGSNR PLSPHITIYS WSLPMAMSIC HRGTGIALSA GVSLFGMSA LLLPGNFESY LELVKSLCLG PALIHTAKFA LVFPLMYHTW NGIRHLMWDL GKGLKIPQLY QSGVVVLVLT V LSSMGLAA M

UniProtKB: Succinate dehydrogenase cytochrome b560 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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.06399 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAVLWRLSAV CGALGGRALL LRTPVVRPAH ISAFLQDRPI PEWCGVQHIH LSPSHHSGSK AASLHWTSER VVSVLLLGLL PAAYLNPCS AMDYSLAAAL TLHGHWGLGQ VVTDYVHGDA LQKAAKAGLL ALSALTFAGL CYFNYHDVGI CKAVAMLWKL

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: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 6 / 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 #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #8: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #9: UBIQUINONE-1

MacromoleculeName: UBIQUINONE-1 / type: ligand / ID: 9 / Number of copies: 1 / Formula: UQ1
Molecular weightTheoretical: 250.29 Da
Chemical component information

ChemComp-UQ1:
UBIQUINONE-1

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Macromolecule #10: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 10 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #11: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 11 / Number of copies: 1 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114967
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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