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Yorodumi- EMDB-15033: Cryo-EM structure of "BC react" conformation of Lactococcus lacti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15033 | |||||||||
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Title | Cryo-EM structure of "BC react" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Tetramer / carboxylase / biotin / LIGASE | |||||||||
Function / homology | Function and homology information pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.41 Å | |||||||||
Authors | Lopez-Alonso JP / Lazaro M / Gil D / Choi PH / Tong L / Valle M | |||||||||
Funding support | France, Spain, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: CryoEM structural exploration of catalytically active enzyme pyruvate carboxylase. Authors: Jorge Pedro López-Alonso / Melisa Lázaro / David Gil-Cartón / Philip H Choi / Alexandra Dodu / Liang Tong / Mikel Valle / Abstract: Pyruvate carboxylase (PC) is a tetrameric enzyme that contains two active sites per subunit that catalyze two consecutive reactions. A mobile domain with an attached prosthetic biotin links both ...Pyruvate carboxylase (PC) is a tetrameric enzyme that contains two active sites per subunit that catalyze two consecutive reactions. A mobile domain with an attached prosthetic biotin links both reactions, an initial biotin carboxylation and the subsequent carboxyl transfer to pyruvate substrate to produce oxaloacetate. Reaction sites are at long distance, and there are several co-factors that play as allosteric regulators. Here, using cryoEM we explore the structure of active PC tetramers focusing on active sites and on the conformational space of the oligomers. The results capture the mobile domain at both active sites and expose catalytic steps of both reactions at high resolution, allowing the identification of substrates and products. The analysis of catalytically active PC tetramers reveals the role of certain motions during enzyme functioning, and the structural changes in the presence of additional cofactors expose the mechanism for allosteric regulation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15033.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-15033-v30.xml emd-15033.xml | 22.5 KB 22.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15033_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_15033.png | 139.7 KB | ||
Masks | emd_15033_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-15033.cif.gz | 7.1 KB | ||
Others | emd_15033_half_map_1.map.gz emd_15033_half_map_2.map.gz | 80.9 MB 81 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15033 | HTTPS FTP |
-Validation report
Summary document | emd_15033_validation.pdf.gz | 165.7 KB | Display | EMDB validaton report |
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Full document | emd_15033_full_validation.pdf.gz | 165.3 KB | Display | |
Data in XML | emd_15033_validation.xml.gz | 497 B | Display | |
Data in CIF | emd_15033_validation.cif.gz | 374 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15033 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15033 | HTTPS FTP |
-Related structure data
Related structure data | 7zz3MC 7zyyC 7zyzC 7zz0C 7zz1C 7zz2C 7zz4C 7zz5C 7zz6C 7zz8C C: citing same article (ref.) M: atomic model generated by this map |
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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_15033.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15033_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15033_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15033_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Pyruvate carboxylase with acetyl coenzyme A
+Supramolecule #1: Pyruvate carboxylase with acetyl coenzyme A
+Macromolecule #1: Pyruvate carboxylase
+Macromolecule #2: BIOTIN
+Macromolecule #3: MAGNESIUM ION
+Macromolecule #4: MANGANESE (II) ION
+Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #6: ACETYL COENZYME *A
+Macromolecule #7: PYRUVIC ACID
+Macromolecule #8: BICARBONATE ION
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #10: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Concentration | 0.05 mg/mL | |||||||||||||||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10518 / Average exposure time: 3.99 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |