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- EMDB-12104: Cryo-EM structure of the dihydrolipoyl transacetylase cubic core ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12104 | |||||||||
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Title | Cryo-EM structure of the dihydrolipoyl transacetylase cubic core of the E. coli pyruvate dehydrogenase complex including lipoyl domains | |||||||||
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Function / homology | ![]() pyruvate catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Skerlova J / Stenmark P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Authors: Jana Škerlová / Jens Berndtsson / Hendrik Nolte / Martin Ott / Pål Stenmark / ![]() ![]() Abstract: The pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A. PDHc encompasses three enzymatically active subunits, namely ...The pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A. PDHc encompasses three enzymatically active subunits, namely pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Dihydrolipoyl transacetylase is a multidomain protein comprising a varying number of lipoyl domains, a peripheral subunit-binding domain, and a catalytic domain. It forms the structural core of the complex, provides binding sites for the other enzymes, and shuffles reaction intermediates between the active sites through covalently bound lipoyl domains. The molecular mechanism by which this shuttling occurs has remained elusive. Here, we report a cryo-EM reconstruction of the native E. coli dihydrolipoyl transacetylase core in a resting state. This structure provides molecular details of the assembly of the core and reveals how the lipoyl domains interact with the core at the active site. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 97.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.1 KB 24.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 90.7 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Others | ![]() ![]() | 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b9kMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12104_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12104_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : dihydrolipoyl transacetylase cubic core of the pyruvate dehydroge...
Entire | Name: dihydrolipoyl transacetylase cubic core of the pyruvate dehydrogenase complex |
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Components |
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-Supramolecule #1: dihydrolipoyl transacetylase cubic core of the pyruvate dehydroge...
Supramolecule | Name: dihydrolipoyl transacetylase cubic core of the pyruvate dehydrogenase complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Dihydrolipoyllysine-residue acetyltransferase component of pyruva...
Macromolecule | Name: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex type: protein_or_peptide / ID: 1 / Details: Lysine 248 covalently modified by dihydrolipoate / Number of copies: 24 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 66.363203 KDa |
Sequence | String: MAIEIKVPDI GADEVEITEI LVKVGDKVEA EQSLITVEGD KASMEVPSPQ AGIVKEIKVS VGDKTQTGAL IMIFDSADGA ADAAPAQAE EKKEAAPAAA PAAAAAKDVN VPDIGSDEVE VTEILVKVGD KVEAEQSLIT VEGDKASMEV PAPFAGTVKE I KVNVGDKV ...String: MAIEIKVPDI GADEVEITEI LVKVGDKVEA EQSLITVEGD KASMEVPSPQ AGIVKEIKVS VGDKTQTGAL IMIFDSADGA ADAAPAQAE EKKEAAPAAA PAAAAAKDVN VPDIGSDEVE VTEILVKVGD KVEAEQSLIT VEGDKASMEV PAPFAGTVKE I KVNVGDKV STGSLIMVFE VAGEAGAAAP AAKQEAAPAA APAPAAGVKE VNVPDIGGDE VEVTEVMVKV GDKVAAEQSL IT VEGD(LA2)AS MEVPAPFAGV VKELKVNVGD KVKTGSLIMI FEVEGAAPAA APAKQEAAAP APAAKAEAPA AAPAAKAEG KSEFAENDAY VHATPLIRRL AREFGVNLAK VKGTGRKGRI LREDVQAYVK EAIKRAEAAP AATGGGIPGM LPWPKVDFSK FGEIEEVEL GRIQKISGAN LSRNWVMIPH VTHFDKTDIT ELEAFRKQQN EEAAKRKLDV KITPVVFIMK AVAAALEQMP R FNSSLSED GQRLTLKKYI NIGVAVDTPN GLVVPVFKDV NKKGIIELSR ELMTISKKAR DGKLTAGEMQ GGCFTISSIG GL GTTHFAP IVNAPEVAIL GVSKSAMEPV WNGKEFVPRL MLPISLSFDH RVIDGADGAR FITIINNTLS DIRRLVM |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation #1
Preparation ID | 1 | |||||||||
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Concentration | 0.6 mg/mL | |||||||||
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time. |
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Sample preparation #2
Preparation ID | 2 | |||||||||
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Concentration | 1.4 mg/mL | |||||||||
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time. |
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Sample preparation #3
Preparation ID | 3 | |||||||||
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Concentration | 0.7 mg/mL | |||||||||
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time. |
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Electron microscopy #1
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Microscopy ID | 1 |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3708 / Average electron dose: 30.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #1~
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Microscopy ID | 1 |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3558 / Average electron dose: 28.11 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #1~~
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Microscopy ID | 1 |
Image recording | Image recording ID: 3 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 12867 / Average electron dose: 28.11 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |