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Yorodumi- EMDB-17126: E. coli pyruvate dehydrogenase (E1) in complex with dihydrolipoam... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17126 | |||||||||
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Title | E. coli pyruvate dehydrogenase (E1) in complex with dihydrolipoamide acetyltransferase (E2) peripheral subunit-binding domain. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | pyruvate dehydrogenase complex / PDHc / E1 / cryo-EM / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information pyruvate catabolic process / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / lipoic acid binding / pyruvate dehydrogenase complex / pyruvate metabolic process / acetyltransferase activity / glycolytic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
Authors | Zdanowicz R / Meinhold S / Glockshuber R | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Dimerization of a 5-kDa domain defines the architecture of the 5-MDa gammaproteobacterial pyruvate dehydrogenase complex. Authors: Sarah Meinhold / Rafal Zdanowicz / Christoph Giese / Rudi Glockshuber / Abstract: The pyruvate dehydrogenase complex (PDHc) is a ~5 MDa assembly of the catalytic subunits pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). ...The pyruvate dehydrogenase complex (PDHc) is a ~5 MDa assembly of the catalytic subunits pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The PDHc core is a cubic complex of eight E2 homotrimers. Homodimers of the peripheral subunits E1 and E3 associate with the core by binding to the peripheral subunit binding domain (PSBD) of E2. Previous reports indicated that 12 E1 dimers and 6 E3 dimers bind to the 24-meric E2 core. Using an assembly arrested E2 homotrimer (E2), we show that two of the three PSBDs in the E2 dimerize, that each PSBD dimer cooperatively binds two E1 dimers, and that E3 dimers only bind to the unpaired PSBD in E2. This mechanism is preserved in wild-type PDHc, with an E1 dimer:E2 monomer:E3 dimer stoichiometry of 16:24:8. The conserved PSBD dimer interface indicates that PSBD dimerization is the previously unrecognized architectural determinant of gammaproteobacterial PDHc megacomplexes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17126.map.gz | 11.3 MB | EMDB map data format | |
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Header (meta data) | emd-17126-v30.xml emd-17126.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17126_fsc.xml | 6.7 KB | Display | FSC data file |
Images | emd_17126.png | 100 KB | ||
Filedesc metadata | emd-17126.cif.gz | 5.8 KB | ||
Others | emd_17126_half_map_1.map.gz emd_17126_half_map_2.map.gz | 20.7 MB 20.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17126 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17126 | HTTPS FTP |
-Related structure data
Related structure data | 8oqjC 8orbC 8osyC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17126.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.584 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17126_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17126_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E. coli pyruvate dehydrogenase (E1) in complex with trimeric dihy...
Entire | Name: E. coli pyruvate dehydrogenase (E1) in complex with trimeric dihydrolipoamide acetyltransferase (E2) of the pyruvate dehydrogenase complex |
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Components |
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-Supramolecule #1: E. coli pyruvate dehydrogenase (E1) in complex with trimeric dihy...
Supramolecule | Name: E. coli pyruvate dehydrogenase (E1) in complex with trimeric dihydrolipoamide acetyltransferase (E2) of the pyruvate dehydrogenase complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Wild-type E2 protein was N- and C-terminally truncated to generate trimeric E2 complexes without lipoyl domains |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Pyruvate dehydrogenase E1 component
Macromolecule | Name: Pyruvate dehydrogenase E1 component / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: pyruvate dehydrogenase (acetyl-transferring) |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SERFPNDVDP IETRDWLQAI ESVIREEGVE RAQYLIDQLL AEARKGGVNV AAGTGISNYI NTIPVEEQPE YPGNLELERR IRSAIRWNAI MTVLRASKKD LELGGHMASF QSSATIYDVC FNHFFRARNE QDGGDLVYFQ GHISPGVYAR AFLEGRLTQE QLDNFRQEVH ...String: SERFPNDVDP IETRDWLQAI ESVIREEGVE RAQYLIDQLL AEARKGGVNV AAGTGISNYI NTIPVEEQPE YPGNLELERR IRSAIRWNAI MTVLRASKKD LELGGHMASF QSSATIYDVC FNHFFRARNE QDGGDLVYFQ GHISPGVYAR AFLEGRLTQE QLDNFRQEVH GNGLSSYPHP KLMPEFWQFP TVSMGLGPIG AIYQAKFLKY LEHRGLKDTS KQTVYAFLGD GEMDEPESKG AITIATREKL DNLVFVINCN LQRLDGPVTG NGKIINELEG IFEGAGWNVI KVMWGSRWDE LLRKDTSGKL IQLMNETVDG DYQTFKSKDG AYVREHFFGK YPETAALVAD WTDEQIWALN RGGHDPKKIY AAFKKAQETK GKATVILAHT IKGYGMGDAA EGKNIAHQVK KMNMDGVRHI RDRFNVPVSD ADIEKLPYIT FPEGSEEHTY LHAQRQKLHG YLPSRQPNFT EKLELPSLQD FGALLEEQSK EISTTIAFVR ALNVMLKNKS IKDRLVPIIA DEARTFGMEG LFRQIGIYSP NGQQYTPQDR EQVAYYKEDE KGQILQEGIN ELGAGCSWLA AATSYSTNNL PMIPFYIYYS MFGFQRIGDL CWAAGDQQAR GFLIGGTSGR TTLNGEGLQH EDGHSHIQSL TIPNCISYDP AYAYEVAVIM HDGLERMYGE KQENVYYYIT TLNENYHMPA MPEGAEEGIR KGIYKLETIE GSKGKVQLLG SGSILRHVRE AAEILAKDYG VGSDVYSVTS FTELARDGQD CERWNMLHPL ETPRVPYIAQ VMNDAPAVAS TDYMKLFAEQ VRTYVPADDY RVLGTDGFGR SDSRENLRHH FEVDASYVVV AALGELAKRG EIDKKVVADA IAKFNIDADK VNPRLA |
-Macromolecule #2: Dihydrolipoyllysine-residue acetyltransferase component of pyruva...
Macromolecule | Name: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MEGKSEFAEN DAYVHATPLI RRLAREFGVN LAKVKGTGRK GRILREDVQA YVKEAIKRAE AAPAATGGGI PGMLPWPKVD FSKFGEIEEV ELGRIQKISG ANLSRNWVMI PHVTHFDKTD ITELEAFRKQ QNEEAAKRKL DVKITPVVFI MKAVAAALEQ MPRFNSSLSE ...String: MEGKSEFAEN DAYVHATPLI RRLAREFGVN LAKVKGTGRK GRILREDVQA YVKEAIKRAE AAPAATGGGI PGMLPWPKVD FSKFGEIEEV ELGRIQKISG ANLSRNWVMI PHVTHFDKTD ITELEAFRKQ QNEEAAKRKL DVKITPVVFI MKAVAAALEQ MPRFNSSLSE DGQRLTLKKY INIGVAVDTP NGLVVPVFKD VNKKGIIELS RELMTISKKA RDGKLTAGEM QGGCFTISSI GGLGTTHFAP IVNAPEVAIL GVSKSAMEPV WNGKEFVPRL MLPISLSFDH RVIDGADGAR FITIINNTLS DIRRL UniProtKB: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 80.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT |