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- EMDB-17452: Single particle cryo-EM structure of the homohexameric 2-oxogluta... -
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Open data
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Basic information
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Title | Single particle cryo-EM structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum | |||||||||
![]() | OdhAFL DM_main map | |||||||||
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![]() | 2-oxoglutarate dehydrogenase / ODH / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.17 Å | |||||||||
![]() | Yang L / Mechaly AM / Bellinzoni M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Authors: Lu Yang / Tristan Wagner / Ariel Mechaly / Alexandra Boyko / Eduardo M Bruch / Daniela Megrian / Francesca Gubellini / Pedro M Alzari / Marco Bellinzoni / ![]() ![]() ![]() ![]() Abstract: Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), ...Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI. #1: ![]() Title: High resolution cryo-EM and crystallographic snapshots of the large actinobacterial 2-oxoglutarate dehydrogenase: an all-in-one fusion with unique properties Authors: Yang L / Wagner T / Mechaly A / Boyko A / Bruch E / Megrian D / Gubellini F / Alzari P / Bellinzoni M | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 148.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.1 KB 20.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 72.2 KB | ||
Others | ![]() ![]() | 200.1 MB 200.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p5tMC ![]() 8p5rC ![]() 8p5sC ![]() 8p5uC ![]() 8p5vC ![]() 8p5wC ![]() 8p5xC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | OdhAFL DM_main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: OdhAFL half map B cryoSPARC
File | emd_17452_half_map_1.map | ||||||||||||
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Annotation | OdhAFL_half_map_B_cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: OdhAFL half map A cryoSPARC
File | emd_17452_half_map_2.map | ||||||||||||
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Annotation | OdhAFL_half_map_A_cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Homohexameric 2-oxoglutarate dehydrogenase
Entire | Name: Homohexameric 2-oxoglutarate dehydrogenase |
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Components |
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-Supramolecule #1: Homohexameric 2-oxoglutarate dehydrogenase
Supramolecule | Name: Homohexameric 2-oxoglutarate dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 808 KDa |
-Macromolecule #1: 2-oxoglutarate dehydrogenase E1/E2 component
Macromolecule | Name: 2-oxoglutarate dehydrogenase E1/E2 component / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO EC number: oxoglutarate dehydrogenase (succinyl-transferring) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 134.972078 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSMSSASTFG QNAWLVDEMF QQFQKDPKSV DKEWRELFEA QGGPNTTPAT TEAQPSAPKE SAKPAPKAAP AAKAAPRVET KPADKTAPK AKESSVPQQP KLPEPGQTPI RGIFKSIAKN MDISLEIPTA TSVRDMPARL MFENRAMVND QLKRTRGGKI S FTHIIGYA ...String: GSMSSASTFG QNAWLVDEMF QQFQKDPKSV DKEWRELFEA QGGPNTTPAT TEAQPSAPKE SAKPAPKAAP AAKAAPRVET KPADKTAPK AKESSVPQQP KLPEPGQTPI RGIFKSIAKN MDISLEIPTA TSVRDMPARL MFENRAMVND QLKRTRGGKI S FTHIIGYA MVKAVMAHPD MNNSYDVIDG KPTLIVPEHI NLGLAIDLPQ KDGSRALVVA AIKETEKMNF SEFLAAYEDI VA RSRKGKL TMDDYQGVTV SLTNPGGIGT RHSVPRLTKG QGTIIGVGSM DYPAEFQGAS EDRLAELGVG KLVTITSTYD HRV IQGAVS GEFLRTMSRL LTDDSFWDEI FDAMNVPYTP MRWAQDVPNT GVDKNTRVMQ LIEAYRSRGH LIADTNPLSW VQPG MPVPD HRDLDIETHN LTIWDLDRTF NVGGFGGKET MTLREVLSRL RAAYTLKVGS EYTHILDRDE RTWLQDRLEA GMPKP TQAE QKYILQKLNA AEAFENFLQT KYVGQKRFSL EGAEALIPLM DSAIDTAAGQ GLDEVVIGMP HRGRLNVLFN IVGKPL ASI FNEFEGQMEQ GQIGGSGDVK YHLGSEGQHL QMFGDGEIKV SLTANPSHLE AVNPVMEGIV RAKQDYLDKG VDGKTVV PL LLHGDAAFAG LGIVPETINL AKLRGYDVGG TIHIVVNNQI GFTTTPDSSR SMHYATDYAK AFGCPVFHVN GDDPEAVV W VGQLATEYRR RFGKDVFIDL VCYRLRGHNE ADDPSMTQPK MYELITGRET VRAQYTEDLL GRGDLSNEDA EAVVRDFHD QMESVFNEVK EGGKKQAEAQ TGITGSQKLP HGLETNISRE ELLELGQAFA NTPEGFNYHP RVAPVAKKRV SSVTEGGIDW AWGELLAFG SLANSGRLVR LAGEDSRRGT FTQRHAVAID PATAEEFNPL HELAQSKGNN GKFLVYNSAL TEYAGMGFEY G YSVGNEDS IVAWEAQFGD FANGAQTIID EYVSSGEAKW GQTSKLILLL PHGYEGQGPD HSSARIERFL QLCAEGSMTV AQ PSTPANH FHLLRRHALS DLKRPLVIFT PKSMLRNKAA ASAPEDFTEV TKFQSVINDP NVADAAKVKK VMLVSGKLYY ELA KRKEKD GRDDIAIVRI EMLHPIPFNR ISEALAGYPN AEEVLFVQDE PANQGPWPFY QEHLPELIPN MPKMRRVSRR AQSS TATGV AKVHQLEEKQ LIDEAFEA UniProtKB: 2-oxoglutarate dehydrogenase E1/E2 component |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: ACETYL COENZYME *A
Macromolecule | Name: ACETYL COENZYME *A / type: ligand / ID: 3 / Number of copies: 6 / Formula: ACO |
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Molecular weight | Theoretical: 809.571 Da |
Chemical component information | ![]() ChemComp-ACO: |
-Macromolecule #4: THIAMINE DIPHOSPHATE
Macromolecule | Name: THIAMINE DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: TPP |
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Molecular weight | Theoretical: 425.314 Da |
Chemical component information | ![]() ChemComp-TPP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 12.0 mg/mL | ||||||
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Buffer | pH: 7.5 / Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 13348 / Average exposure time: 1.75 sec. / Average electron dose: 40.0 e/Å2 / Details: Each image was composed by 40 frames |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |