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- EMDB-62932: Cryo-EM structure of the apo-form succinate dehydrogenase from Ch... -

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Entry
Database: EMDB / ID: EMD-62932
TitleCryo-EM structure of the apo-form succinate dehydrogenase from Chloroflexus aurantiacus
Map data
Sample
  • Complex: The apo-form succinate dehydrogenase from Chloroflexus aurantiacus
    • Protein or peptide: x 3 types
  • Ligand: x 9 types
KeywordsSuccinate: menaquinone oxidoreductase / membrane protein / complex II / electron transfer
Function / homology
Function and homology information


steroid dehydrogenase activity, acting on the CH-CH group of donors / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity ...steroid dehydrogenase activity, acting on the CH-CH group of donors / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
Succinate dehydrogenase cytochrome b558 subunit / Succinate dehydrogenase/fumarate reductase flavoprotein subunit, low-GC Gram-positive bacteria / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 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 cytochrome b558 subunit / Succinate dehydrogenase/fumarate reductase flavoprotein subunit, low-GC Gram-positive bacteria / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 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 / 4Fe-4S dicluster domain / 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
4Fe-4S ferredoxin iron-sulfur binding domain protein / succinate dehydrogenase / Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsZhang X / Wu JY / Xu XL
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471270 China
National Natural Science Foundation of China (NSFC)32171227 China
National Natural Science Foundation of China (NSFC)31870740 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of menaquinone reduction by succinate dehydrogenase from Chloroflexus aurantiacus.
Authors: Xin Zhang / Jingyi Wu / Jiamao Wang / Huimin He / Aokun Liu / Xin Hong / Yuanyi Yu / Xinkai Pei / Xianjie Fang / Yueyong Xin / Lu Yu / Changlin Tian / Xiaoling Xu /
Abstract: Succinate: menaquinone oxidoreductase (SQR) couples the oxidation of succinate with the reduction of menaquinone (MK) as part of the TCA cycle and the aerobic respiratory chain in MK-containing ...Succinate: menaquinone oxidoreductase (SQR) couples the oxidation of succinate with the reduction of menaquinone (MK) as part of the TCA cycle and the aerobic respiratory chain in MK-containing bacteria and archaea. Despite its significance, questions persist regarding the electron and proton transfer mechanisms that drive the endergonic MK reduction by succinate. In this study, we determine cryo-EM structures of succinate dehydrogenase (SDH) from Chloroflexus aurantiacus (CaSDH), a facultative filamentous anoxygenic phototroph (FAP) that forms one of the earliest branches of photosynthetic bacteria. The structures of trimeric CaSDH, resolved in both apo- and MK-bound forms, reveal a single membrane-anchoring subunit containing two b-type hemes, a canonical Q site, and a Q site with atypical location, configuration and specificity, each bound to MK molecules. Using structural analysis, EPR, and enzymatic assays, we uncover electron transfer pathways connecting succinate oxidation to MK reduction at the Q and Q sites. These findings provide structural insights into the electron and proton transfer mechanisms of MK-dependent diheme SQRs and establish a foundation for structure-based inhibitor design and antibacterial drug development targeting these enzymes.
History
DepositionJan 2, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62932.png

Downloads & links

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Map

FileDownload / File: emd_62932.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.4544187 - 2.3317757
Average (Standard dev.)0.00376671 (±0.09497107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62932_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_62932_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : The apo-form succinate dehydrogenase from Chloroflexus aurantiacus

EntireName: The apo-form succinate dehydrogenase from Chloroflexus aurantiacus
Components
  • Complex: The apo-form succinate dehydrogenase from Chloroflexus aurantiacus
    • Protein or peptide: Succinate dehydrogenase or fumarate reductase, flavoprotein subunit
    • Protein or peptide: 4Fe-4S ferredoxin iron-sulfur binding domain protein
    • Protein or peptide: Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: SUCCINIC ACID
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: The apo-form succinate dehydrogenase from Chloroflexus aurantiacus

SupramoleculeName: The apo-form succinate dehydrogenase from Chloroflexus aurantiacus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)

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Macromolecule #1: Succinate dehydrogenase or fumarate reductase, flavoprotein subunit

MacromoleculeName: Succinate dehydrogenase or fumarate reductase, flavoprotein subunit
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: ec: 1.3.99.1
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 73.37393 KDa
SequenceString: MSETKNETTV RTGTRQVEYV SVLDSKVPTG PIEQRWDKHR FEMKLVNPAN RRKYTIIVVG SGLAGASAAA TLGEAGYNVL CFCYQDSPR RAHSIAAQGG INAAKNYRND GDSIYRLFYD TVKGGDFRAR ESNVYRLAQV SVNIIDQCVA QGVPFAREYG G LLDNRSFG ...String:
MSETKNETTV RTGTRQVEYV SVLDSKVPTG PIEQRWDKHR FEMKLVNPAN RRKYTIIVVG SGLAGASAAA TLGEAGYNVL CFCYQDSPR RAHSIAAQGG INAAKNYRND GDSIYRLFYD TVKGGDFRAR ESNVYRLAQV SVNIIDQCVA QGVPFAREYG G LLDNRSFG GAQVARTFYA RGQTGQQLLL GAYQALSRQI AAGTVKMFPR TEMLDLVVVD GRARGIITRD MVTGKITRYA AD AVVLATG GYGNVFYLST NAKGCNATAI WRAHRRGAFF GNPCFTQIHP TCIPVSGEYQ SKLTLMSESL RNDGRIWVPK KKG DTRRPQ DIPESERDYY LEERYPSFGN LVPRDIASRA AKQVCDEGRG VGPGGLGVYL DFADAIKRLG RQKIAERYGN LFDM YKQIT GEDPYETPMR IYPAVHYTMG GLWVDYNLQS TIPGLFVIGE ANFSDHGANR LGASALMQGL ADGYFILPYT IANFL AQVK PGGVSIDRPE FAEAEAEINQ RIQRLLSIRG KRTVDSFHRE LGKLMWDKCG MARNAAGLRE ALQRIPEIRA EFWENV NVP GEANDLNQAL EKAGRVADFL ELAELMCLDA LHREESCGGH FREEYQTPDG EALRNDEQFS YVAAWEFTGD LAKPRLH KE PLVFEYVKPT QRSYK

UniProtKB: succinate dehydrogenase

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Macromolecule #2: 4Fe-4S ferredoxin iron-sulfur binding domain protein

MacromoleculeName: 4Fe-4S ferredoxin iron-sulfur binding domain protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 28.110371 KDa
SequenceString: MKITLKIWRQ KNRNTPGEFK TYVMDNVNPD MSFLEMLDVL NEDLMSRGEE PVAFDHDCRE GICGMCSLMI NGVAHGPKNA ITTCQLHMR SFKDGDTITV EPWRASAFPI LKDLVVDRSA FDRIIQAGGY ISVSTGSAPD ANTIPVSKVA ADRAMDAAAC I GCGACVAA ...String:
MKITLKIWRQ KNRNTPGEFK TYVMDNVNPD MSFLEMLDVL NEDLMSRGEE PVAFDHDCRE GICGMCSLMI NGVAHGPKNA ITTCQLHMR SFKDGDTITV EPWRASAFPI LKDLVVDRSA FDRIIQAGGY ISVSTGSAPD ANTIPVSKVA ADRAMDAAAC I GCGACVAA CPNGSAMLFT AAKVTHLALL PQGQPERYQR VVNMVAQADF EGFGNCTNIG ECAAVCPKEI SLETIAQLNR DL VMAALRG IEPNTPIVPA TTR

UniProtKB: 4Fe-4S ferredoxin iron-sulfur binding domain protein

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Macromolecule #3: Succinate dehydrogenase (Or fumarate reductase) cytochrome b subu...

MacromoleculeName: Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 27.14168 KDa
SequenceString: MTGVLTLTRT SVGKKVIMAL TGFVLVGFVV FHMYGNLKMY QGPEVYNAYA AGLRELGYPI FGHEHLLWIA RFILLASVFL HIWAATSLT LQSRRSLQAS SISTVRRYGQ HKRQSGYADY TMRFGGVLIF FFIIYHILHL TFGVVGYEPG QFIHPHGDVY E TYNNVVYG ...String:
MTGVLTLTRT SVGKKVIMAL TGFVLVGFVV FHMYGNLKMY QGPEVYNAYA AGLRELGYPI FGHEHLLWIA RFILLASVFL HIWAATSLT LQSRRSLQAS SISTVRRYGQ HKRQSGYADY TMRFGGVLIF FFIIYHILHL TFGVVGYEPG QFIHPHGDVY E TYNNVVYG FQNPLIVGFY LLTMVFLALH LYHGVWSMFQ TLGWNNRTYD RLLRGLAIVV AAAVFIGNIS FPLAVYFGFV A

UniProtKB: Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family

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Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 3 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

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

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Macromolecule #5: SUCCINIC ACID

MacromoleculeName: SUCCINIC ACID / type: ligand / ID: 5 / Number of copies: 3 / Formula: SIN
Molecular weightTheoretical: 118.088 Da
Chemical component information

ChemComp-SIN:
SUCCINIC ACID

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Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 7 / Number of copies: 3 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #8: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 8 / Number of copies: 3 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #9: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 9 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #10: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 10 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #11: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 11 / Number of copies: 3 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

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Macromolecule #12: (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: 12 / Number of copies: 3 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6lum

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51634
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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